diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 4ecfbfe3..b290e090 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -10,15 +10,7 @@ "vscode": { // Set *default* container specific settings.json values on container create. "settings": { - "python.defaultInterpreterPath": "/opt/conda/bin/python", - "python.linting.enabled": true, - "python.linting.pylintEnabled": true, - "python.formatting.autopep8Path": "/opt/conda/bin/autopep8", - "python.formatting.yapfPath": "/opt/conda/bin/yapf", - "python.linting.flake8Path": "/opt/conda/bin/flake8", - "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle", - "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle", - "python.linting.pylintPath": "/opt/conda/bin/pylint" + "python.defaultInterpreterPath": "/opt/conda/bin/python" }, // Add the IDs of extensions you want installed when the container is created. diff --git a/.editorconfig b/.editorconfig index b6b31907..72dda289 100644 --- a/.editorconfig +++ b/.editorconfig @@ -18,7 +18,16 @@ end_of_line = unset insert_final_newline = unset trim_trailing_whitespace = unset indent_style = unset -indent_size = unset +[/subworkflows/nf-core/**] +charset = unset +end_of_line = unset +insert_final_newline = unset +trim_trailing_whitespace = unset +indent_style = unset [/assets/email*] indent_size = unset + +# ignore python and markdown +[*.{py,md}] +indent_style = unset diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 38618636..1a51bc53 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -9,9 +9,8 @@ Please use the pre-filled template to save time. However, don't be put off by this template - other more general issues and suggestions are welcome! Contributions to the code are even more welcome ;) -:::info -If you need help using or modifying nf-core/methylseq then the best place to ask is on the nf-core Slack [#methylseq](https://nfcore.slack.com/channels/methylseq) channel ([join our Slack here](https://nf-co.re/join/slack)). -::: +> [!NOTE] +> If you need help using or modifying nf-core/methylseq then the best place to ask is on the nf-core Slack [#methylseq](https://nfcore.slack.com/channels/methylseq) channel ([join our Slack here](https://nf-co.re/join/slack)). ## Contribution workflow @@ -20,15 +19,18 @@ If you'd like to write some code for nf-core/methylseq, the standard workflow is 1. Check that there isn't already an issue about your idea in the [nf-core/methylseq issues](https://github.com/nf-core/methylseq/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/methylseq repository](https://github.com/nf-core/methylseq) to your GitHub account 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) -4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). +4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/). ## Tests -You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to -receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir `. +You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command: + +```bash +nf-test test --profile debug,test,docker --verbose +``` When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. @@ -38,7 +40,7 @@ There are typically two types of tests that run: ### Lint tests `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to. -To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint ` command. +To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint ` command. If any failures or warnings are encountered, please follow the listed URL for more documentation. @@ -73,7 +75,7 @@ If you wish to contribute a new step, please use the following coding standards: 2. Write the process block (see below). 3. Define the output channel if needed (see below). 4. Add any new parameters to `nextflow.config` with a default (see below). -5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool). +5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool). 6. Add sanity checks and validation for all relevant parameters. 7. Perform local tests to validate that the new code works as expected. 8. If applicable, add a new test command in `.github/workflow/ci.yml`. @@ -84,13 +86,13 @@ If you wish to contribute a new step, please use the following coding standards: Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope. -Once there, use `nf-core schema build` to add to `nextflow_schema.json`. +Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`. ### Default processes resource requirements -Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. +Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. -The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block. +The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block. ### Naming schemes @@ -101,7 +103,7 @@ Please use the following naming schemes, to make it easy to understand what is g ### Nextflow version bumping -If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]` +If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]` ### Images and figures diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 1000a8aa..36c0c759 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -17,7 +17,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/meth - [ ] If you've fixed a bug or added code that should be tested, add tests! - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/methylseq/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/methylseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. -- [ ] Make sure your code lints (`nf-core lint`). +- [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 81a346ca..c68b5424 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -1,22 +1,40 @@ name: nf-core AWS full size tests -# This workflow is triggered on published releases. +# This workflow is triggered on PRs opened against the master branch. # It can be additionally triggered manually with GitHub actions workflow dispatch button. # It runs the -profile 'test_full' on AWS batch on: - release: - types: [published] + pull_request: + branches: + - master workflow_dispatch: + pull_request_review: + types: [submitted] + jobs: - run-tower: + run-platform: name: Run AWS full tests - if: github.repository == 'nf-core/methylseq' + # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered + if: github.repository == 'nf-core/methylseq' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch' runs-on: ubuntu-latest strategy: matrix: aligner: ["bismark", "bismark_hisat", "bwameth"] steps: - - name: Launch workflow via tower + - uses: octokit/request-action@v2.x + if: github.event_name != 'workflow_dispatch' + id: check_approvals + with: + route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100 + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + - id: test_variables + if: github.event_name != 'workflow_dispatch' + run: | + JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}' + CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length') + test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required + - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} @@ -27,14 +45,14 @@ jobs: parameters: | { "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/methylseq/results-${{ github.sha }}/${{matrix.aligner}}" + "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/methylseq/results-${{ github.sha }}/${{matrix.aligner}}", "aligner": "${{ matrix.aligner }}", } profiles: test_full - - uses: actions/upload-artifact@v3 + - uses: actions/upload-artifact@v4 with: - name: Tower debug log file + name: Seqera Platform debug log file path: | - tower_action_*.log - tower_action_*.json + seqera_platform_action_*.log + seqera_platform_action_*.json diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 635dbc04..5c96ee94 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -5,7 +5,7 @@ name: nf-core AWS test on: workflow_dispatch: jobs: - run-tower: + run-platform: name: Run AWS tests if: github.repository == 'nf-core/methylseq' runs-on: ubuntu-latest @@ -13,8 +13,8 @@ jobs: matrix: aligner: ["bismark", "bismark_hisat", "bwameth"] steps: - # Launch workflow using Tower CLI tool action - - name: Launch workflow via tower + # Launch workflow using Seqera Platform CLI tool action + - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} @@ -29,9 +29,9 @@ jobs: } profiles: test - - uses: actions/upload-artifact@v3 + - uses: actions/upload-artifact@v4 with: - name: Tower debug log file + name: Seqera Platform debug log file path: | - tower_action_*.log - tower_action_*.json + seqera_platform_action_*.log + seqera_platform_action_*.json diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index 32d20557..65022865 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -19,7 +19,7 @@ jobs: # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets - name: Post PR comment if: failure() - uses: mshick/add-pr-comment@v1 + uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 with: message: | ## This PR is against the `master` branch :x: diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index a9126136..468812a9 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,124 +1,119 @@ -# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors name: nf-core CI +# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors on: push: branches: - - "dev" + - dev pull_request: - branches: - - "dev" - - "master" release: - types: - - "published" + types: [published] + workflow_dispatch: env: NXF_ANSI_LOG: false - NFTEST_VER: "0.8.2" + NFT_VER: "0.9.0" + NFT_WORKDIR: "~" + NFT_DIFF: "pdiff" + NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2" + NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity + NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" cancel-in-progress: true jobs: - list: - name: List Tests - if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/methylseq') }}" - outputs: - # Expose matched filters as job 'modules' output variable - tests: ${{ steps.list.outputs.tests }} - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - - - name: Setup Nextflow - uses: nf-core/setup-nextflow@v1 - - - name: Install nf-test - if: steps.cache-software.outputs.cache-hit != 'true' - run: | - wget -qO- https://code.askimed.com/install/nf-test | bash - sudo mv nf-test /usr/local/bin/ - - - name: List nf-test - id: list - run: | - echo "tests=$(nf-test list --silent --format=json)" >> "$GITHUB_OUTPUT" - test: - name: ${{ matrix.tags }} (${{ matrix.profile }}-${{ matrix.NXF_VER }}) + name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})" # Only run on push if this is the nf-core dev branch (merged PRs) - if: needs.list.outputs.tests != '[]' - needs: [list] + if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/methylseq') }}" runs-on: ubuntu-latest strategy: + fail-fast: false matrix: NXF_VER: - - "23.04.0" + - "24.04.2" - "latest-everything" - profile: ["docker"] # TODO , "singularity", "conda"] - test: ["${{ fromJson(needs.list.outputs.tests) }}"] + shard: [1, 2, 3, 4, 5] + filter: [pipeline, workflow] + profile: + - "docker" + - "singularity" + test_name: + - "test" + isMaster: + - ${{ github.base_ref == 'master' }} + # Exclude conda and singularity on dev exclude: - - test: "tests/subworkflows/local/grohmm/main.nf.test@3508b8c9" - - test: "tests/subworkflows/local/grohmm/main.nf.test@716555be" - - test: "tests/subworkflows/local/grohmm/main.nf.test@306b4b15" + - isMaster: false + profile: "conda" + - isMaster: false + profile: "singularity" steps: - name: Check out pipeline code - uses: actions/checkout@v4 - - - name: Cache Nextflow installation - id: cache-software - uses: actions/cache@v3 + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 with: - path: | - /usr/local/bin/nf-test - /home/runner/.nf-test/nf-test.jar - key: methylseq-${{ runner.os }}-${{ matrix.NXF_VER }} + fetch-depth: 0 - - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + - name: Set up Nextflow + uses: nf-core/setup-nextflow@v2 with: version: "${{ matrix.NXF_VER }}" - - name: Install nf-test - if: steps.cache-software.outputs.cache-hit != 'true' + - name: Install pdiff to see diff between nf-test snapshots run: | - wget -qO- https://code.askimed.com/install/nf-test | bash - sudo mv nf-test /usr/local/bin/ + python -m pip install --upgrade pip + pip install pdiff + + - uses: nf-core/setup-nf-test@v1 + with: + version: ${{ env.NFT_VER }} + + - name: Set up Apptainer + if: matrix.profile == 'singularity' + uses: eWaterCycle/setup-apptainer@main - name: Set up Singularity if: matrix.profile == 'singularity' - uses: eWaterCycle/setup-singularity@v5 - with: - singularity-version: 3.7.1 + run: | + mkdir -p $NXF_SINGULARITY_CACHEDIR + mkdir -p $NXF_SINGULARITY_LIBRARYDIR - - name: Set up miniconda + - name: Set up Miniconda if: matrix.profile == 'conda' - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 with: + miniconda-version: "latest" auto-update-conda: true - channels: conda-forge,bioconda,defaults - python-version: ${{ matrix.python-version }} + conda-solver: libmamba + channels: conda-forge,bioconda - - name: Conda clean + - name: Set up Conda if: matrix.profile == 'conda' - run: conda clean -a + run: | + echo $(realpath $CONDA)/condabin >> $GITHUB_PATH + echo $(realpath python) >> $GITHUB_PATH - - name: Run nf-test + - name: Clean up Disk space + uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 + + - name: Run Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }}) run: | nf-test test \ - --profile="test,${{ matrix.profile }}" \ - ${{ matrix.test }} \ - --junitxml=${{ matrix.test }}-${{ matrix.profile }}.xml - - - name: Publish Test Report - uses: mikepenz/action-junit-report@v3 - if: success() || failure() # run this step even if previous step failed - with: - path: ${{ matrix.test }}-${{ matrix.profile }}.xml + --ci \ + --shard ${{ matrix.shard }}/${{ strategy.job-total }} \ + --changed-since HEAD^ \ + --profile "+${{ matrix.profile }}" \ + --filter ${{ matrix.filter }} - name: Output log on failure if: failure() run: | sudo apt install bat > /dev/null - batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml + batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log + + - name: Publish Test Report + uses: mikepenz/action-junit-report@v3 + if: always() # always run even if the previous step fails + with: + report_paths: test.xml diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml index 694e90ec..0b6b1f27 100644 --- a/.github/workflows/clean-up.yml +++ b/.github/workflows/clean-up.yml @@ -10,7 +10,7 @@ jobs: issues: write pull-requests: write steps: - - uses: actions/stale@v7 + - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9 with: stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml new file mode 100644 index 00000000..713dc3e7 --- /dev/null +++ b/.github/workflows/download_pipeline.yml @@ -0,0 +1,119 @@ +name: Test successful pipeline download with 'nf-core pipelines download' + +# Run the workflow when: +# - dispatched manually +# - when a PR is opened or reopened to master branch +# - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. +on: + workflow_dispatch: + inputs: + testbranch: + description: "The specific branch you wish to utilize for the test execution of nf-core pipelines download." + required: true + default: "dev" + pull_request: + types: + - opened + - edited + - synchronize + branches: + - master + pull_request_target: + branches: + - master + +env: + NXF_ANSI_LOG: false + +jobs: + download: + runs-on: ubuntu-latest + steps: + - name: Install Nextflow + uses: nf-core/setup-nextflow@v2 + + - name: Disk space cleanup + uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 + + - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + with: + python-version: "3.12" + architecture: "x64" + + - name: Setup Apptainer + uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0 + with: + apptainer-version: 1.3.4 + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install git+https://github.com/nf-core/tools.git@dev + + - name: Get the repository name and current branch set as environment variable + run: | + echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV} + echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} + echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} + + - name: Make a cache directory for the container images + run: | + mkdir -p ./singularity_container_images + + - name: Download the pipeline + env: + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images + run: | + nf-core pipelines download ${{ env.REPO_LOWERCASE }} \ + --revision ${{ env.REPO_BRANCH }} \ + --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ + --compress "none" \ + --container-system 'singularity' \ + --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \ + --container-cache-utilisation 'amend' \ + --download-configuration 'yes' + + - name: Inspect download + run: tree ./${{ env.REPOTITLE_LOWERCASE }} + + - name: Count the downloaded number of container images + id: count_initial + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Initial container image count: $image_count" + echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV} + + - name: Run the downloaded pipeline (stub) + id: stub_run_pipeline + continue-on-error: true + env: + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images + NXF_SINGULARITY_HOME_MOUNT: true + run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results + - name: Run the downloaded pipeline (stub run not supported) + id: run_pipeline + if: ${{ job.steps.stub_run_pipeline.status == failure() }} + env: + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images + NXF_SINGULARITY_HOME_MOUNT: true + run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results + + - name: Count the downloaded number of container images + id: count_afterwards + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Post-pipeline run container image count: $image_count" + echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV} + + - name: Compare container image counts + run: | + if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then + initial_count=${{ env.IMAGE_COUNT_INITIAL }} + final_count=${{ env.IMAGE_COUNT_AFTER }} + difference=$((final_count - initial_count)) + echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!" + tree ./singularity_container_images + exit 1 + else + echo "The pipeline can be downloaded successfully!" + fi diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index 5430f37a..c7ffc80c 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -4,7 +4,7 @@ on: types: [created] jobs: - deploy: + fix-linting: # Only run if comment is on a PR with the main repo, and if it contains the magic keywords if: > contains(github.event.comment.html_url, '/pull/') && @@ -13,10 +13,17 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@v4 + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 with: token: ${{ secrets.nf_core_bot_auth_token }} + # indication that the linting is being fixed + - name: React on comment + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + comment-id: ${{ github.event.comment.id }} + reactions: eyes + # Action runs on the issue comment, so we don't get the PR by default # Use the gh cli to check out the PR - name: Checkout Pull Request @@ -24,32 +31,59 @@ jobs: env: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} - - uses: actions/setup-node@v4 + # Install and run pre-commit + - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + with: + python-version: "3.12" - - name: Install Prettier - run: npm install -g prettier @prettier/plugin-php + - name: Install pre-commit + run: pip install pre-commit - # Check that we actually need to fix something - - name: Run 'prettier --check' - id: prettier_status - run: | - if prettier --check ${GITHUB_WORKSPACE}; then - echo "result=pass" >> $GITHUB_OUTPUT - else - echo "result=fail" >> $GITHUB_OUTPUT - fi + - name: Run pre-commit + id: pre-commit + run: pre-commit run --all-files + continue-on-error: true - - name: Run 'prettier --write' - if: steps.prettier_status.outputs.result == 'fail' - run: prettier --write ${GITHUB_WORKSPACE} + # indication that the linting has finished + - name: react if linting finished succesfully + if: steps.pre-commit.outcome == 'success' + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + comment-id: ${{ github.event.comment.id }} + reactions: "+1" - name: Commit & push changes - if: steps.prettier_status.outputs.result == 'fail' + id: commit-and-push + if: steps.pre-commit.outcome == 'failure' run: | git config user.email "core@nf-co.re" git config user.name "nf-core-bot" git config push.default upstream git add . git status - git commit -m "[automated] Fix linting with Prettier" + git commit -m "[automated] Fix code linting" git push + + - name: react if linting errors were fixed + id: react-if-fixed + if: steps.commit-and-push.outcome == 'success' + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + comment-id: ${{ github.event.comment.id }} + reactions: hooray + + - name: react if linting errors were not fixed + if: steps.commit-and-push.outcome == 'failure' + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + comment-id: ${{ github.event.comment.id }} + reactions: confused + + - name: react if linting errors were not fixed + if: steps.commit-and-push.outcome == 'failure' + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + issue-number: ${{ github.event.issue.number }} + body: | + @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually. + See [CI log](https://github.com/nf-core/methylseq/actions/runs/${{ github.run_id }}) for more details. diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 905c58e4..a502573c 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -1,6 +1,6 @@ name: nf-core linting # This workflow is triggered on pushes and PRs to the repository. -# It runs the `nf-core lint` and markdown lint tests to ensure +# It runs the `nf-core pipelines lint` and markdown lint tests to ensure # that the code meets the nf-core guidelines. on: push: @@ -11,87 +11,62 @@ on: types: [published] jobs: - EditorConfig: + pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - - uses: actions/setup-node@v4 - - - name: Install editorconfig-checker - run: npm install -g editorconfig-checker - - - name: Run ECLint check - run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile') - - Prettier: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - - uses: actions/setup-node@v4 - - - name: Install Prettier - run: npm install -g prettier - - - name: Run Prettier --check - run: prettier --check ${GITHUB_WORKSPACE} - - PythonBlack: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - - name: Check code lints with Black - uses: psf/black@stable - - # If the above check failed, post a comment on the PR explaining the failure - - name: Post PR comment - if: failure() - uses: mshick/add-pr-comment@v1 + - name: Set up Python 3.12 + uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: - message: | - ## Python linting (`black`) is failing - - To keep the code consistent with lots of contributors, we run automated code consistency checks. - To fix this CI test, please run: - - * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black` - * Fix formatting errors in your pipeline: `black .` + python-version: "3.12" - Once you push these changes the test should pass, and you can hide this comment :+1: + - name: Install pre-commit + run: pip install pre-commit - We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help! - - Thanks again for your contribution! - repo-token: ${{ secrets.GITHUB_TOKEN }} - allow-repeats: false + - name: Run pre-commit + run: pre-commit run --all-files nf-core: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@v4 + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@v2 - - uses: actions/setup-python@v4 + - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: - python-version: "3.11" + python-version: "3.12" architecture: "x64" + - name: read .nf-core.yml + uses: pietrobolcato/action-read-yaml@1.1.0 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yml + - name: Install dependencies run: | python -m pip install --upgrade pip - pip install nf-core + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + + - name: Run nf-core pipelines lint + if: ${{ github.base_ref != 'master' }} + env: + GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} + run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - - name: Run nf-core lint + - name: Run nf-core pipelines lint --release + if: ${{ github.base_ref == 'master' }} env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} - run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md + run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - name: Save PR number if: ${{ always() }} @@ -99,7 +74,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 0bbcd30f..42e519bf 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@v2 + uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6 with: workflow: linting.yml workflow_conclusion: completed @@ -21,7 +21,7 @@ jobs: run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - name: Post PR comment - uses: marocchino/sticky-pull-request-comment@v2 + uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2 with: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} number: ${{ steps.pr_number.outputs.pr_number }} diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 6ad33927..c6ba35df 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -9,6 +9,11 @@ jobs: toot: runs-on: ubuntu-latest steps: + - name: get topics and convert to hashtags + id: get_topics + run: | + echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT + - uses: rzr/fediverse-action@master with: access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} @@ -20,11 +25,13 @@ jobs: Please see the changelog: ${{ github.event.release.html_url }} + ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics + send-tweet: runs-on: ubuntu-latest steps: - - uses: actions/setup-python@v4 + - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: python-version: "3.10" - name: Install dependencies @@ -56,7 +63,7 @@ jobs: bsky-post: runs-on: ubuntu-latest steps: - - uses: zentered/bluesky-post-action@v0.0.2 + - uses: zentered/bluesky-post-action@80dbe0a7697de18c15ad22f4619919ceb5ccf597 # v0.1.0 with: post: | Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml new file mode 100644 index 00000000..e8aafe44 --- /dev/null +++ b/.github/workflows/template_version_comment.yml @@ -0,0 +1,46 @@ +name: nf-core template version comment +# This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version. +# It posts a comment to the PR, even if it comes from a fork. + +on: pull_request_target + +jobs: + template_version: + runs-on: ubuntu-latest + steps: + - name: Check out pipeline code + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + with: + ref: ${{ github.event.pull_request.head.sha }} + + - name: Read template version from .nf-core.yml + uses: nichmor/minimal-read-yaml@v0.0.2 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yml + + - name: Install nf-core + run: | + python -m pip install --upgrade pip + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + + - name: Check nf-core outdated + id: nf_core_outdated + run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV} + + - name: Post nf-core template version comment + uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 + if: | + contains(env.OUTPUT, 'nf-core') + with: + repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }} + allow-repeats: false + message: | + > [!WARNING] + > Newer version of the nf-core template is available. + > + > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. + > Please update your pipeline to the latest version. + > + > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). + # diff --git a/.gitignore b/.gitignore index 4a37b601..fd2afe07 100644 --- a/.gitignore +++ b/.gitignore @@ -6,7 +6,6 @@ results/ testing/ testing* *.pyc -.vscode -.nf-test +null/ .nf-test.log -test-datasets/ +.nf-test/ diff --git a/.gitpod.yml b/.gitpod.yml index acf72695..1591998e 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -1,21 +1,23 @@ -image: nfcore/gitpod:latest +image: nfcore/gitpod:dev tasks: - name: Update Nextflow and setup pre-commit command: | pre-commit install --install-hooks nextflow self-update + - name: conda update + command: | + conda update --all --yes - name: unset JAVA_TOOL_OPTIONS command: | unset JAVA_TOOL_OPTIONS + vscode: extensions: # based on nf-core.nf-core-extensionpack - - codezombiech.gitignore # Language support for .gitignore files - # - cssho.vscode-svgviewer #Β SVG viewer - - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed + #- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - mechatroner.rainbow-csv # Highlight columns in csv files in different colors - # - nextflow.nextflow # Nextflow syntax highlighting + - nextflow.nextflow # Nextflow syntax highlighting - oderwat.indent-rainbow # Highlight indentation level - streetsidesoftware.code-spell-checker # Spelling checker for source code + - charliermarsh.ruff # Code linter Ruff diff --git a/.nf-core.yml b/.nf-core.yml index 61d85c35..1eee6001 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,8 +1,22 @@ -repository_type: pipeline +bump_version: null lint: - files_unchanged: - - .gitattributes + actions_ci: false files_exist: - - bin/markdown_to_html.py - actions_ci: False - multiqc_config: False + - lib/nfcore_external_java_deps.jar + - conf/modules.config + modules_config: false +nf_core_version: 3.0.2 +org_path: null +repository_type: pipeline +template: + author: Phil Ewels, Sateesh Peri + description: Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, + part of the nf-core community. + force: false + is_nfcore: true + name: methylseq + org: nf-core + outdir: . + skip_features: null + version: 2.7.0 +update: null diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 0c31cdb9..9e9f0e1c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,5 +1,13 @@ repos: - repo: https://github.com/pre-commit/mirrors-prettier - rev: "v2.7.1" + rev: "v3.1.0" hooks: - id: prettier + additional_dependencies: + - prettier@3.2.5 + + - repo: https://github.com/editorconfig-checker/editorconfig-checker.python + rev: "3.0.3" + hooks: + - id: editorconfig-checker + alias: ec diff --git a/CHANGELOG.md b/CHANGELOG.md index ecff842f..22560fce 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,34 @@ # nf-core/methylseq +## [v2.7.0](https://github.com/nf-core/methylseq/releases/tag/2.7.0) - [2024-10-25] + +### Bug fixes & refactoring + +- πŸ”„ Updated template to nf-core/tools v2.12 [#377](https://github.com/nf-core/methylseq/pull/377) +- πŸ”„ Updated template to nf-core/tools v2.13 [#380](https://github.com/nf-core/methylseq/pull/380) +- πŸ”„ Updated template to nf-core/tools v2.13.1 [#384](https://github.com/nf-core/methylseq/pull/384) +- πŸ”„ Updated template to nf-core/tools v2.14.1 [#399](https://github.com/nf-core/methylseq/pull/399) +- πŸ”„ Updated template to nf-core/tools v3.0.2 [#426](https://github.com/nf-core/methylseq/pull/426) +- πŸ› fix sample/replicate merge [#401](https://github.com/nf-core/methylseq/pull/401) +- πŸ› fix fasta reference usage [#403](https://github.com/nf-core/methylseq/pull/403) +- πŸ› fix missing type field in nextflow_schema.json (issue-#361) [#417](https://github.com/nf-core/methylseq/pull/417) +- πŸ› fix samtools sort overwrites (issue-#328) [#414](https://github.com/nf-core/methylseq/pull/414) +- πŸ› fix bwameth pipeline skipping all bwameth steps when --fasta, --fasta_index, and --bwa_meth_index are provided. (issue-#396) [#414](https://github.com/nf-core/methylseq/pull/414) +- πŸ› fix typo in samplesheet in README and usage doc (issue-#391) [#414](https://github.com/nf-core/methylseq/pull/418) +- πŸ› stage fasta separately from the index folders for bismark & bwameth. Fixes issue with using a local copy of fasta (issue-#305) [#428](https://github.com/nf-core/methylseq/pull/428) +- πŸ› fix bismark, bwameth align modules + other module updates + update snaps [#432](https://github.com/nf-core/methylseq/pull/432) + +### Pipeline Updates + +- πŸ”§ Updated nf-core modules for preseq [#390](https://github.com/nf-core/methylseq/pull/390) +- πŸ”§ Added new trimgalore length_trim param [#416](https://github.com/nf-core/methylseq/pull/416) +- πŸ”§ Updated nf-core modules [#414](https://github.com/nf-core/methylseq/pull/414) +- πŸ”§ Updated nf-core sub-workflows [#414](https://github.com/nf-core/methylseq/pull/414) +- πŸ”§ Removed `conf/modules.config` and introduce separate `nextflow.config` [#414](https://github.com/nf-core/methylseq/pull/414) +- πŸ”§ Added sub-workflow & pipeline level nf-tests [#414](https://github.com/nf-core/methylseq/pull/414) +- πŸ”§ Pipeline metro map added by @Shaun-Regenbaum , @FelixKrueger , @ewels [#438](https://github.com/nf-core/methylseq/pull/438) +- πŸ”§ Add Bismark HISAT2 index to igenomes [#444](https://github.com/nf-core/methylseq/pull/444) + ## [v2.6.0](https://github.com/nf-core/methylseq/releases/tag/2.6.0) - 2024-01-05 ### Bug fixes & refactoring diff --git a/LICENSE b/LICENSE index 1e87cfa3..6ae63b3c 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) Phil Ewels +Copyright (c) Phil Ewels, Sateesh Peri Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index 0b928113..00202575 100644 --- a/README.md +++ b/README.md @@ -1,14 +1,19 @@ -# ![nf-core/methylseq](docs/images/nf-core-methylseq_logo_light.png#gh-light-mode-only) ![nf-core/methylseq](docs/images/nf-core-methylseq_logo_dark.png#gh-dark-mode-only) - -[![GitHub Actions CI Status](https://github.com/nf-core/methylseq/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/methylseq/actions?query=workflow%3A%22nf-core+CI%22) -[![GitHub Actions Linting Status](https://github.com/nf-core/methylseq/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/methylseq/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/methylseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1343417-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1343417) - -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) +

+ + + nf-core/methylseq + +

+ +[![GitHub Actions CI Status](https://github.com/nf-core/methylseq/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/methylseq/actions/workflows/ci.yml) +[![GitHub Actions Linting Status](https://github.com/nf-core/methylseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/methylseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/methylseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1343417-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1343417) +[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) + +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) -[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/methylseq) -[![nf-test](https://img.shields.io/badge/tested_with-nf--test-337ab7.svg)](https://github.com/askimed/nf-test) +[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/methylseq) [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23methylseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/methylseq)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) @@ -16,6 +21,8 @@ **nf-core/methylseq** is a bioinformatics analysis pipeline used for Methylation (Bisulfite) sequencing data. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results. +![nf-core/methylseq metro map](docs/images/metromap.png) + The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker / Singularity containers making installation trivial and results highly reproducible. On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/methylseq/results). @@ -23,22 +30,23 @@ On release, automated continuous integration tests run the pipeline on a full-si ## Pipeline Summary The pipeline allows you to choose between running either [Bismark](https://github.com/FelixKrueger/Bismark) or [bwa-meth](https://github.com/brentp/bwa-meth) / [MethylDackel](https://github.com/dpryan79/methyldackel). + Choose between workflows by using `--aligner bismark` (default, uses bowtie2 for alignment), `--aligner bismark_hisat` or `--aligner bwameth`. -| Step | Bismark workflow | bwa-meth workflow | -| -------------------------------------------- | ---------------- | --------------------- | -| Generate Reference Genome Index _(optional)_ | Bismark | bwa-meth | -| Merge re-sequenced FastQ files | cat | cat | -| Raw data QC | FastQC | FastQC | -| Adapter sequence trimming | Trim Galore! | Trim Galore! | -| Align Reads | Bismark | bwa-meth | -| Deduplicate Alignments | Bismark | Picard MarkDuplicates | -| Extract methylation calls | Bismark | MethylDackel | -| Sample report | Bismark | - | -| Summary Report | Bismark | - | -| Alignment QC | Qualimap | Qualimap | -| Sample complexity | Preseq | Preseq | -| Project Report | MultiQC | MultiQC | +| Step | Bismark workflow | bwa-meth workflow | +| -------------------------------------------- | ------------------------ | --------------------- | +| Generate Reference Genome Index _(optional)_ | Bismark | bwa-meth | +| Merge re-sequenced FastQ files | cat | cat | +| Raw data QC | FastQC | FastQC | +| Adapter sequence trimming | Trim Galore! | Trim Galore! | +| Align Reads | Bismark (bowtie2/hisat2) | bwa-meth | +| Deduplicate Alignments | Bismark | Picard MarkDuplicates | +| Extract methylation calls | Bismark | MethylDackel | +| Sample report | Bismark | - | +| Summary Report | Bismark | - | +| Alignment QC | Qualimap | Qualimap | +| Sample complexity | Preseq | Preseq | +| Project Report | MultiQC | MultiQC | ## Usage @@ -50,11 +58,11 @@ First, prepare a samplesheet with your input data that looks as follows: `samplesheet.csv`: ```csv -sample,fastq_1,fastq_2 -SRR389222_sub1,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz -SRR389222_sub2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz -SRR389222_sub2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz -Ecoli_10K_methylated,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz +sample,fastq_1,fastq_2,genome +SRR389222_sub1,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz,, +SRR389222_sub2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz,, +SRR389222_sub3,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz,, +Ecoli_10K_methylated,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz, ``` Each row represents a fastq file (single-end) or a pair of fastq files (paired end). @@ -66,8 +74,7 @@ nextflow run nf-core/methylseq --input samplesheet.csv --outdir --genom ``` > [!WARNING] -> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; -> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). +> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files). For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/methylseq/usage) and the [parameter documentation](https://nf-co.re/methylseq/parameters). @@ -91,6 +98,7 @@ These scripts were originally written for use at the [National Genomics Infrastr - Rickard HammarΓ©n ([@Hammarn](https://github.com/Hammarn/)) - Alexander Peltzer ([@apeltzer](https://github.com/apeltzer/)) - Patrick HΓΌther ([@phue](https://github.com/phue/)) + - Maxime U Garcia ([@maxulysse](https://github.com/maxulysse/)) ## Contributions and Support diff --git a/assets/email_template.html b/assets/email_template.html index f0081ad9..264df06c 100644 --- a/assets/email_template.html +++ b/assets/email_template.html @@ -12,7 +12,7 @@ -

nf-core/methylseq v${version}

+

nf-core/methylseq ${version}

Run Name: $runName

<% if (!success){ diff --git a/assets/email_template.txt b/assets/email_template.txt index 82ca1dc6..d8e55c6c 100644 --- a/assets/email_template.txt +++ b/assets/email_template.txt @@ -4,7 +4,7 @@ |\\ | |__ __ / ` / \\ |__) |__ } { | \\| | \\__, \\__/ | \\ |___ \\`-._,-`-, `._,._,' - nf-core/methylseq v${version} + nf-core/methylseq ${version} ---------------------------------------------------- Run Name: $runName diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index c6e99955..37078f04 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/methylseq + This report has been generated by the nf-core/methylseq analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-methylseq-methods-description": order: -1000 @@ -11,6 +11,9 @@ report_section_order: order: -1002 export_plots: true + +disable_version_detection: true + table_columns_visible: QualiMap: avg_gc: false diff --git a/assets/nf-core-methylseq_logo_light.png b/assets/nf-core-methylseq_logo_light.png index cae5ed6a..1067bdf9 100644 Binary files a/assets/nf-core-methylseq_logo_light.png and b/assets/nf-core-methylseq_logo_light.png differ diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv index aa6b7542..ee7324b3 100644 --- a/assets/samplesheet.csv +++ b/assets/samplesheet.csv @@ -2,4 +2,4 @@ sample,fastq_1,fastq_2,genome SRR389222_sub1,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz,, SRR389222_sub2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz,, SRR389222_sub3,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz,, -Ecoli,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz, +Ecoli_10K_methylated,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz, diff --git a/assets/schema_input.json b/assets/schema_input.json index 9e51e2e9..cc4330d8 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/nf-core/methylseq/master/assets/schema_input.json", "title": "nf-core/methylseq pipeline - params.input schema", "description": "Schema for the file provided with params.input", @@ -21,20 +21,18 @@ "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" }, "fastq_2": { - "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'", "type": "string", "format": "file-path", "exists": true, - "anyOf": [ - { - "type": "string", - "pattern": "^\\S+\\.f(ast)?q\\.gz$" - }, - { - "type": "string", - "maxLength": 0 - } - ] + "pattern": "^\\S+\\.f(ast)?q\\.gz$", + "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" + }, + "genome": { + "type": "string", + "format": "file-path", + "exists": true, + "pattern": "^[a-zA-Z0-9._-]+$", + "errorMessage": "Invalid reference genome name" } }, "required": ["sample", "fastq_1"] diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py deleted file mode 100755 index da1e666f..00000000 --- a/bin/check_samplesheet.py +++ /dev/null @@ -1,263 +0,0 @@ -#!/usr/bin/env python - - -"""Provide a command line tool to validate and transform tabular samplesheets.""" - - -import argparse -import csv -import logging -import sys -from collections import Counter -from pathlib import Path - -logger = logging.getLogger() - - -class RowChecker: - """ - Define a service that can validate and transform each given row. - - Attributes: - modified (list): A list of dicts, where each dict corresponds to a previously - validated and transformed row. The order of rows is maintained. - - """ - - VALID_FORMATS = ( - ".fq.gz", - ".fastq.gz", - ) - - def __init__( - self, - sample_col="sample", - first_col="fastq_1", - second_col="fastq_2", - single_col="single_end", - **kwargs, - ): - """ - Initialize the row checker with the expected column names. - - Args: - sample_col (str): The name of the column that contains the sample name - (default "sample"). - first_col (str): The name of the column that contains the first (or only) - FASTQ file path (default "fastq_1"). - second_col (str): The name of the column that contains the second (if any) - FASTQ file path (default "fastq_2"). - single_col (str): The name of the new column that will be inserted and - records whether the sample contains single- or paired-end sequencing - reads (default "single_end"). - - """ - super().__init__(**kwargs) - self._sample_col = sample_col - self._first_col = first_col - self._second_col = second_col - self._single_col = single_col - self._seen = set() - self.modified = [] - - def validate_and_transform(self, row): - """ - Perform all validations on the given row and insert the read pairing status. - - Args: - row (dict): A mapping from column headers (keys) to elements of that row - (values). - - """ - self._validate_sample(row) - self._validate_first(row) - self._validate_second(row) - self._validate_pair(row) - self._seen.add((row[self._sample_col], row[self._first_col])) - self.modified.append(row) - - def _validate_sample(self, row): - """Assert that the sample name exists and convert spaces to underscores.""" - if len(row[self._sample_col]) <= 0: - raise AssertionError("Sample input is required.") - # Sanitize samples slightly. - row[self._sample_col] = row[self._sample_col].replace(" ", "_") - - def _validate_first(self, row): - """Assert that the first FASTQ entry is non-empty and has the right format.""" - if len(row[self._first_col]) <= 0: - raise AssertionError("At least the first FASTQ file is required.") - self._validate_fastq_format(row[self._first_col]) - - def _validate_second(self, row): - """Assert that the second FASTQ entry has the right format if it exists.""" - if len(row[self._second_col]) > 0: - self._validate_fastq_format(row[self._second_col]) - - def _validate_pair(self, row): - """Assert that read pairs have the same file extension. Report pair status.""" - if row[self._first_col] and row[self._second_col]: - row[self._single_col] = False - first_col_suffix = Path(row[self._first_col]).suffixes[-2:] - second_col_suffix = Path(row[self._second_col]).suffixes[-2:] - if first_col_suffix != second_col_suffix: - raise AssertionError("FASTQ pairs must have the same file extensions.") - else: - row[self._single_col] = True - - def _validate_fastq_format(self, filename): - """Assert that a given filename has one of the expected FASTQ extensions.""" - if not any(filename.endswith(extension) for extension in self.VALID_FORMATS): - raise AssertionError( - f"The FASTQ file has an unrecognized extension: {filename}\n" - f"It should be one of: {', '.join(self.VALID_FORMATS)}" - ) - - def validate_unique_samples(self): - """ - Assert that the combination of sample name and FASTQ filename is unique. - - In addition to the validation, also rename all samples to have a suffix of _T{n}, where n is the - number of times the same sample exist, but with different FASTQ files, e.g., multiple runs per experiment. - - """ - if len(self._seen) != len(self.modified): - raise AssertionError("The pair of sample name and FASTQ must be unique.") - seen = Counter() - for row in self.modified: - sample = row[self._sample_col] - seen[sample] += 1 - row[self._sample_col] = f"{sample}_T{seen[sample]}" - - -def read_head(handle, num_lines=10): - """Read the specified number of lines from the current position in the file.""" - lines = [] - for idx, line in enumerate(handle): - if idx == num_lines: - break - lines.append(line) - return "".join(lines) - - -def sniff_format(handle): - """ - Detect the tabular format. - - Args: - handle (text file): A handle to a `text file`_ object. The read position is - expected to be at the beginning (index 0). - - Returns: - csv.Dialect: The detected tabular format. - - .. _text file: - https://docs.python.org/3/glossary.html#term-text-file - - """ - peek = read_head(handle) - handle.seek(0) - sniffer = csv.Sniffer() - dialect = sniffer.sniff(peek) - return dialect - - -def check_samplesheet(file_in, file_out): - """ - Check that the tabular samplesheet has the structure expected by nf-core pipelines. - - Validate the general shape of the table, expected columns, and each row. Also add - an additional column which records whether one or two FASTQ reads were found. - - Args: - file_in (pathlib.Path): The given tabular samplesheet. The format can be either - CSV, TSV, or any other format automatically recognized by ``csv.Sniffer``. - file_out (pathlib.Path): Where the validated and transformed samplesheet should - be created; always in CSV format. - - Example: - This function checks that the samplesheet follows the following structure, - see also the `viral recon samplesheet`_:: - - sample,fastq_1,fastq_2 - SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz - SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz - SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq.gz, - - .. _viral recon samplesheet: - https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv - - """ - required_columns = {"sample", "fastq_1", "fastq_2"} - # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`. - with file_in.open(newline="") as in_handle: - dialect = sniff_format(in_handle) - logger.info(f"Detected samplesheet format: '{dialect.delimiter}'") - reader = csv.DictReader(in_handle, dialect=dialect) - # Validate the existence of the expected header columns. - if not required_columns.issubset(reader.fieldnames): - req_cols = ", ".join(required_columns) - logger.critical(f"The sample sheet **must** contain these column headers: {req_cols}") - logger.critical(f"Found the following: {', '.join(reader.fieldnames)}") - sys.exit(1) - # Validate each row. - checker = RowChecker() - for i, row in enumerate(reader): - try: - checker.validate_and_transform(row) - except AssertionError as error: - logger.critical(f"{str(error)} On line {i + 2}.") - sys.exit(1) - # Ties into FastQ merging process - checker.validate_unique_samples() - header = list(reader.fieldnames) - header.insert(1, "single_end") - # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`. - with file_out.open(mode="w", newline="") as out_handle: - writer = csv.DictWriter(out_handle, header, delimiter=",") - writer.writeheader() - for row in checker.modified: - writer.writerow(row) - - -def parse_args(argv=None): - """Define and immediately parse command line arguments.""" - parser = argparse.ArgumentParser( - description="Validate and transform a tabular samplesheet.", - epilog="Example: python check_samplesheet.py samplesheet.csv samplesheet.valid.csv", - ) - parser.add_argument( - "file_in", - metavar="FILE_IN", - type=Path, - help="Tabular input samplesheet in CSV or TSV format.", - ) - parser.add_argument( - "file_out", - metavar="FILE_OUT", - type=Path, - help="Transformed output samplesheet in CSV format.", - ) - parser.add_argument( - "-l", - "--log-level", - help="The desired log level (default WARNING).", - choices=("CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG"), - default="INFO", - ) - return parser.parse_args(argv) - - -def main(argv=None): - """Coordinate argument parsing and program execution.""" - args = parse_args(argv) - logging.basicConfig(level=args.log_level, format="[%(levelname)s] %(message)s") - if not args.file_in.is_file(): - logger.error(f"The given input file {args.file_in} was not found!") - sys.exit(2) - args.file_out.parent.mkdir(parents=True, exist_ok=True) - check_samplesheet(args.file_in, args.file_out) - - -if __name__ == "__main__": - sys.exit(main()) diff --git a/conf/base.config b/conf/base.config index e19bc5bb..3b0ca369 100644 --- a/conf/base.config +++ b/conf/base.config @@ -11,9 +11,10 @@ nextflow.enable.configProcessNamesValidation = false process { - cpus = { check_max( 1 * task.attempt, 'cpus' ) } - memory = { check_max( 6.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + + cpus = { 1 * task.attempt } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } maxRetries = 1 @@ -26,30 +27,30 @@ process { // adding in your local modules too. // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors withLabel:process_single { - cpus = { check_max( 1 , 'cpus' ) } - memory = { check_max( 6.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 1 } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_low { - cpus = { check_max( 2 * task.attempt, 'cpus' ) } - memory = { check_max( 12.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 2 * task.attempt } + memory = { 12.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_medium { - cpus = { check_max( 6 * task.attempt, 'cpus' ) } - memory = { check_max( 36.GB * task.attempt, 'memory' ) } - time = { check_max( 8.h * task.attempt, 'time' ) } + cpus = { 6 * task.attempt } + memory = { 36.GB * task.attempt } + time = { 8.h * task.attempt } } withLabel:process_high { - cpus = { check_max( 12 * task.attempt, 'cpus' ) } - memory = { check_max( 72.GB * task.attempt, 'memory' ) } - time = { check_max( 16.h * task.attempt, 'time' ) } + cpus = { 12 * task.attempt } + memory = { 72.GB * task.attempt } + time = { 16.h * task.attempt } } withLabel:process_long { - time = { check_max( 20.h * task.attempt, 'time' ) } + time = { 20.h * task.attempt } } withLabel:process_high_memory { - memory = { check_max( 200.GB * task.attempt, 'memory' ) } + memory = { 200.GB * task.attempt } } withLabel:error_ignore { errorStrategy = 'ignore' @@ -58,19 +59,16 @@ process { errorStrategy = 'retry' maxRetries = 2 } - withName:CUSTOM_DUMPSOFTWAREVERSIONS { - cache = false - } withName: BISMARK_ALIGN { - time = { check_max( 8.d * task.attempt, 'time' ) } + time = { 8.d * task.attempt } } withName: BISMARK_DEDUPLICATE { - time = { check_max( 2.d * task.attempt, 'time' ) } + time = { 2.d * task.attempt } } withName: BISMARK_METHYLATIONEXTRACTOR { - time = { check_max( 1.d * task.attempt, 'time' ) } + time = { 1.d * task.attempt } } withName: BWAMETH_ALIGN { - time = { check_max( 6.d * task.attempt, 'time' ) } + time = { 6.d * task.attempt } } } diff --git a/conf/igenomes.config b/conf/igenomes.config index 8442ed57..3edfaa7e 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -13,10 +13,12 @@ params { genomes { 'GRCh37' { fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/" bismark = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/" + bwameth = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BwamethIndex/" gtf = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf" bed12 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed" readme = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt" @@ -25,19 +27,23 @@ params { blacklist = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed" } 'GRCh38' { - fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" + fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa.fai" + bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/" + bowtie2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/" + star = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/" + bismark = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/" + bismark_hisat2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/Hisat2Index/" + bwameth = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BwamethIndex/" + gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf" + bed12 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed" + mito_name = "chrM" + macs_gsize = "2.7e9" + blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" } 'CHM13' { fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/" bwamem2 = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/" gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf" @@ -46,6 +52,7 @@ params { } 'GRCm38' { fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/" @@ -59,6 +66,7 @@ params { } 'TAIR10' { fasta = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/" @@ -70,6 +78,7 @@ params { } 'EB2' { fasta = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/" @@ -80,6 +89,7 @@ params { } 'UMD3.1' { fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/" @@ -91,6 +101,7 @@ params { } 'WBcel235' { fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/" @@ -102,6 +113,7 @@ params { } 'CanFam3.1' { fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/" @@ -113,6 +125,7 @@ params { } 'GRCz10' { fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/" @@ -123,6 +136,7 @@ params { } 'BDGP6' { fasta = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/" @@ -134,6 +148,7 @@ params { } 'EquCab2' { fasta = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/" @@ -145,6 +160,7 @@ params { } 'EB1' { fasta = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/" @@ -155,6 +171,7 @@ params { } 'Galgal4' { fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/" @@ -165,6 +182,7 @@ params { } 'Gm01' { fasta = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/" @@ -175,6 +193,7 @@ params { } 'Mmul_1' { fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/" @@ -186,6 +205,7 @@ params { } 'IRGSP-1.0' { fasta = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/" @@ -196,6 +216,7 @@ params { } 'CHIMP2.1.4' { fasta = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/" @@ -207,6 +228,7 @@ params { } 'Rnor_5.0' { fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/" @@ -217,6 +239,7 @@ params { } 'Rnor_6.0' { fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/" @@ -227,6 +250,7 @@ params { } 'R64-1-1' { fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/" @@ -238,6 +262,7 @@ params { } 'EF2' { fasta = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/" @@ -250,6 +275,7 @@ params { } 'Sbi1' { fasta = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/" @@ -260,6 +286,7 @@ params { } 'Sscrofa10.2' { fasta = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/" @@ -271,6 +298,7 @@ params { } 'AGPv3' { fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/" @@ -281,6 +309,7 @@ params { } 'hg38' { fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/" @@ -293,6 +322,7 @@ params { } 'hg19' { fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/" @@ -306,6 +336,7 @@ params { } 'mm10' { fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/" @@ -319,6 +350,7 @@ params { } 'bosTau8' { fasta = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/" @@ -329,6 +361,7 @@ params { } 'ce10' { fasta = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/" @@ -341,6 +374,7 @@ params { } 'canFam3' { fasta = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/" @@ -352,6 +386,7 @@ params { } 'danRer10' { fasta = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/" @@ -363,6 +398,7 @@ params { } 'dm6' { fasta = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/" @@ -374,6 +410,7 @@ params { } 'equCab2' { fasta = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/" @@ -385,6 +422,7 @@ params { } 'galGal4' { fasta = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/" @@ -396,6 +434,7 @@ params { } 'panTro4' { fasta = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/" @@ -407,6 +446,7 @@ params { } 'rn6' { fasta = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/" @@ -417,6 +457,7 @@ params { } 'sacCer3' { fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/" @@ -427,6 +468,7 @@ params { } 'susScr3' { fasta = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa" + fasta_index = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa.fai" bwa = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/" bowtie2 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/" star = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/" diff --git a/conf/igenomes_ignored.config b/conf/igenomes_ignored.config new file mode 100644 index 00000000..b4034d82 --- /dev/null +++ b/conf/igenomes_ignored.config @@ -0,0 +1,9 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for iGenomes paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Empty genomes dictionary to use when igenomes is ignored. +---------------------------------------------------------------------------------------- +*/ + +params.genomes = [:] diff --git a/conf/modules.config b/conf/modules.config deleted file mode 100755 index 5c55e852..00000000 --- a/conf/modules.config +++ /dev/null @@ -1,468 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Config file for defining DSL2 per module options and publishing paths -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Available keys to override module options: - ext.args = Additional arguments appended to command in module. - ext.args2 = Second set of arguments appended to command in module (multi-tool modules). - ext.args3 = Third set of arguments appended to command in module (multi-tool modules). - ext.prefix = File name prefix for output files. ----------------------------------------------------------------------------------------- -*/ - -process { - - publishDir = [ - path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - - withName: SAMPLESHEET_CHECK { - publishDir = [ - path: { "${params.outdir}/pipeline_info" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: CUSTOM_DUMPSOFTWAREVERSIONS { - publishDir = [ - path: { "${params.outdir}/pipeline_info" }, - mode: params.publish_dir_mode, - pattern: '*_versions.yml' - ] - } - - withName: FASTQC { - ext.args = '--quiet' - publishDir = [ - [ - path: { "${params.outdir}/fastqc" }, - mode: params.publish_dir_mode, - pattern: "*.html" - ], - [ - path: { "${params.outdir}/fastqc/zips" }, - mode: params.publish_dir_mode, - pattern: "*.zip" - ] - ] - } - - withName: TRIMGALORE { - ext.args = { [ - // Static args - '--fastqc', - - // Special flags - params.rrbs ? '--rrbs' : '', - params.nextseq_trim > 0 ? "--nextseq ${params.nextseq_trim}" : '', - - // Trimming - R1 - params.clip_r1 > 0 ? "--clip_r1 ${params.clip_r1}" : ( - params.pbat ? "--clip_r1 9" : ( - (params.single_cell || params.cegx) ? "--clip_r1 6" : ( - params.epignome ? "--clip_r1 8" : ( - (params.accel || params.zymo || params.em_seq) ? "--clip_r1 10" : '' - ) - ) - ) - ), - - // Trimming - R2 - meta.single_end ? '' : ( - params.clip_r2 > 0 ? "--clip_r2 ${params.clip_r2}" : ( - params.pbat ? "--clip_r2 9" : ( - (params.single_cell || params.cegx) ? "--clip_r2 6" : ( - params.epignome ? "--clip_r2 8" : ( - (params.zymo || params.em_seq) ? "--clip_r2 10" : ( - params.accel ? "--clip_r2 15" : '' - ) - ) - ) - ) - ) - ), - - // Trimming - 3' R1 - params.three_prime_clip_r1 > 0 ? "--three_prime_clip_r1 ${params.three_prime_clip_r1}" : ( - params.pbat ? "--three_prime_clip_r1 9" : ( - params.single_cell ? "--three_prime_clip_r1 6" : ( - params.cegx ? "--three_prime_clip_r1 2" : ( - params.epignome ? "--three_prime_clip_r1 8" : ( - (params.accel || params.zymo || params.em_seq) ? "--three_prime_clip_r1 10" : '' - ) - ) - ) - ) - ), - - // Trimming - 3' R2 - meta.single_end ? '' : ( - params.three_prime_clip_r2 > 0 ? "--three_prime_clip_r2 ${params.three_prime_clip_r2}" : ( - params.pbat ? "--three_prime_clip_r2 9" : ( - params.single_cell ? "--three_prime_clip_r2 6" : ( - params.cegx ? "--three_prime_clip_r2 2" : ( - params.epignome ? "--three_prime_clip_r2 8" : ( - (params.accel || params.zymo || params.em_seq) ? "--three_prime_clip_r2 10" : '' - ) - ) - ) - ) - ) - ), - ].join(' ').trim() } - publishDir = [ - [ - path: { "${params.outdir}/trimgalore/fastqc" }, - mode: params.publish_dir_mode, - pattern: "*.html" - ], - [ - path: { "${params.outdir}/trimgalore/fastqc/zips" }, - mode: params.publish_dir_mode, - pattern: "*.zip" - ], - [ - path: { "${params.outdir}/trimgalore" }, - mode: params.publish_dir_mode, - pattern: "*.fq.gz", - enabled: params.save_trimmed - ], - [ - path: { "${params.outdir}/trimgalore/logs" }, - mode: params.publish_dir_mode, - pattern: "*.txt" - ] - ] - } - - withName: BISMARK_GENOMEPREPARATION { - ext.args = [ - params.aligner == 'bismark_hisat' ? ' --hisat2' : ' --bowtie2', - params.slamseq ? ' --slam' : '' - ].join(' ').trim() - publishDir = [ - path: { "${params.outdir}/${params.aligner}/reference_genome" }, - saveAs: { it =~ /.*\.yml/ ? null : it }, - mode: params.publish_dir_mode, - enabled: params.save_reference - ] - } - - withName: BISMARK_ALIGN { - ext.args = { [ - params.aligner == 'bismark_hisat' ? ' --hisat2' : ' --bowtie2', - params.aligner == 'bismark_hisat' && params.known_splices ? " --known-splicesite-infile <(hisat2_extract_splice_sites.py ${known_splices})" : '', - params.pbat ? ' --pbat' : '', - ( params.single_cell || params.non_directional || params.zymo ) ? ' --non_directional' : '', - params.unmapped ? ' --unmapped' : '', - params.relax_mismatches ? " --score_min L,0,-${params.num_mismatches}" : '', - params.local_alignment ? " --local" : '', - !meta.single_end && params.minins ? " --minins ${params.minins}" : '', - meta.single_end ? '' : ( - params.maxins ? " --maxins ${params.maxins}" : ( - params.em_seq ? " --maxins 1000" : '' - ) - ) - ].join(' ').trim() } - publishDir = [ - [ - path: { "${params.outdir}/${params.aligner}/alignments/unmapped" }, - mode: params.publish_dir_mode, - pattern: "*.fq.gz", - enabled: params.unmapped - ], - [ - path: { "${params.outdir}/${params.aligner}/alignments" }, - mode: params.publish_dir_mode, - pattern: "*.bam", - enabled: (params.save_align_intermeds || params.skip_deduplication || params.rrbs) - ], - [ - path: { "${params.outdir}/${params.aligner}/alignments/logs" }, - mode: params.publish_dir_mode, - pattern: "*.txt" - ] - ] - } - - withName: BISMARK_DEDUPLICATE { - ext.args = '' - publishDir = [ - [ - path: { "${params.outdir}/${params.aligner}/deduplicated/logs" }, - mode: params.publish_dir_mode, - pattern: "*.txt" - ], - [ - path: { "${params.outdir}/${params.aligner}/deduplicated" }, - mode: params.publish_dir_mode, - pattern: "*.bam" - ] - ] - } - - withName: BISMARK_METHYLATIONEXTRACTOR { - ext.args = { [ - params.comprehensive ? ' --comprehensive --merge_non_CpG' : '', - params.meth_cutoff ? " --cutoff ${params.meth_cutoff}" : '', - params.nomeseq ? '--CX' : '', - params.ignore_r1 > 0 ? "--ignore ${params.ignore_r1}" : '', - params.ignore_3prime_r1 > 0 ? "--ignore_3prime ${params.ignore_3prime_r1}" : '', - meta.single_end ? '' : (params.no_overlap ? ' --no_overlap' : '--include_overlap'), - meta.single_end ? '' : (params.ignore_r2 > 0 ? "--ignore_r2 ${params.ignore_r2}" : ""), - meta.single_end ? '' : (params.ignore_3prime_r2 > 0 ? "--ignore_3prime_r2 ${params.ignore_3prime_r2}": "") - ].join(' ').trim() } - publishDir = [ - [ - path: { "${params.outdir}/${params.aligner}/methylation_calls/mbias" }, - mode: params.publish_dir_mode, - pattern: "*M-bias.txt" - ], - [ - path: { "${params.outdir}/${params.aligner}/methylation_calls/methylation_coverage" }, - mode: params.publish_dir_mode, - pattern: "*cov.gz" - ], - [ - path: { "${params.outdir}/${params.aligner}/methylation_calls/bedGraph" }, - mode: params.publish_dir_mode, - pattern: "*bedGraph.gz" - ], - [ - path: { "${params.outdir}/${params.aligner}/methylation_calls/splitting_report" }, - mode: params.publish_dir_mode, - pattern: "*splitting_report.txt" - ], - [ - path: { "${params.outdir}/${params.aligner}/methylation_calls/methylation_calls" }, - mode: params.publish_dir_mode, - pattern: "*txt.gz" - ] - ] - } - - withName: BISMARK_COVERAGE2CYTOSINE { - ext.args = params.nomeseq ? '--nome-seq' : '' - publishDir = [ - publishDir = [ - path: { "${params.outdir}/bismark/coverage2cytosine/summaries" }, - mode: params.publish_dir_mode, - pattern: "*_summary.txt" - ], - publishDir = [ - path: { "${params.outdir}/bismark/coverage2cytosine/reports" }, - mode: params.publish_dir_mode, - pattern: "*_report.txt.gz" - ], - publishDir = [ - path: { "${params.outdir}/bismark/coverage2cytosine/coverage" }, - mode: params.publish_dir_mode, - pattern: "*cov.gz" - ] - ] - } - - withName: BISMARK_REPORT { - ext.args = '' - publishDir = [ - path: "${params.outdir}/${params.aligner}/reports", - mode: params.publish_dir_mode, - pattern: "*.html" - ] - } - - - withName: BISMARK_SUMMARY { - ext.args = '' - publishDir = [ - path: "${params.outdir}/${params.aligner}/summary", - mode: params.publish_dir_mode, - pattern: "*.{html,txt}" - ] - } - - withName: BWAMETH_INDEX { - ext.args = '' - publishDir = [ - path: { "${params.outdir}/${params.aligner}/reference_genome" }, - mode: params.publish_dir_mode, - saveAs: { it.equals('versions.yml') ? null : it.tokenize("/").last() }, - enabled: params.save_reference - ] - } - - withName: BWAMETH_ALIGN { - ext.args = '' - publishDir = [ - path: { "${params.outdir}/${params.aligner}/alignments" }, - pattern: "*.bam", - mode: params.publish_dir_mode, - enabled: params.save_align_intermeds - ] - } - - withName: PICARD_MARKDUPLICATES { - ext.args = "--ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --PROGRAM_RECORD_ID 'null' --TMP_DIR tmp" - ext.prefix = { "${meta.id}.markdup.sorted" } - publishDir = [ - [ - path: { "${params.outdir}/${params.aligner}/deduplicated/picard_metrics" }, - pattern: "*.metrics.txt", - mode: params.publish_dir_mode - ], - [ - path: { "${params.outdir}/${params.aligner}/deduplicated" }, - pattern: "*.bam", - mode: params.publish_dir_mode - ] - ] - } - - withName: SAMTOOLS_SORT { - ext.prefix = { "${meta.id}.sorted" } - publishDir = [ - [ - path: { "${params.outdir}/${params.aligner}/deduplicated/" }, - mode: params.publish_dir_mode, - pattern: "*markdup*.bam", - enabled: params.save_align_intermeds - ], - [ - path: { "${params.outdir}/${params.aligner}/alignments/" }, - mode: params.publish_dir_mode, - pattern: "*.bam", - enabled: params.save_align_intermeds - ] - ] - } - - withName: SAMTOOLS_FLAGSTAT { - publishDir = [ - [ - path: { "${params.outdir}/${params.aligner}/alignments/samtools_stats/" }, - mode: params.publish_dir_mode, - pattern: "*.flagstat" - ] - ] - } - - withName: SAMTOOLS_STATS { - publishDir = [ - [ - path: { "${params.outdir}/${params.aligner}/alignments/samtools_stats/" }, - mode: params.publish_dir_mode, - pattern: "*.stats" - ] - ] - } - - withName: SAMTOOLS_FAIDX { - ext.args = "" - publishDir = [ - path: { "${params.outdir}/${params.aligner}/reference_genome" }, - mode: params.publish_dir_mode, - enabled: params.save_reference, - pattern: "*.fai" - ] - } - - withName: SAMTOOLS_INDEX_ALIGNMENTS { - ext.args = "" - publishDir = [ - [ - path: { "${params.outdir}/${params.aligner}/alignments/" }, - mode: params.publish_dir_mode, - pattern: "*.bam*", - enabled: params.save_align_intermeds - ] - ] - } - - withName: SAMTOOLS_INDEX_DEDUPLICATED { - ext.args = "" - publishDir = [ - [ - path: { "${params.outdir}/${params.aligner}/deduplicated/" }, - mode: params.publish_dir_mode, - pattern: "*.bai" - ] - ] - } - - withName: METHYLDACKEL_MBIAS { - ext.args = [ - params.comprehensive ? ' --CHG --CHH' : '', - params.ignore_flags ? " --ignoreFlags" : '' - ].join(" ").trim() - publishDir = [ - [ - path: { "${params.outdir}/methyldackel/mbias" }, - mode: params.publish_dir_mode, - pattern: "*mbias.txt" - ] - ] - } - - withName: METHYLDACKEL_EXTRACT { - ext.args = [ - params.comprehensive ? ' --CHG --CHH' : '', - params.ignore_flags ? " --ignoreFlags" : '', - params.methyl_kit ? " --methylKit" : '', - params.min_depth > 0 ? " --minDepth ${params.min_depth}" : '' - ].join(" ").trim() - publishDir = [ - [ - path: { "${params.outdir}/methyldackel" }, - mode: params.publish_dir_mode, - pattern: "*.bedGraph" - ], - [ - path: { "${params.outdir}/methyldackel" }, - mode: params.publish_dir_mode, - pattern: "*.methylKit" - ] - ] - } - - withName: QUALIMAP_BAMQC { - ext.args = [ - params.genome.toString().startsWith('GRCh') ? '-gd HUMAN' : '', - params.genome.toString().startsWith('GRCm') ? '-gd MOUSE' : '' - ].join(" ").trim() - } - - withName: PRESEQ_LCEXTRAP { - ext.args = " -verbose -bam" - publishDir = [ - [ - path: { "${params.outdir}/${params.aligner}/preseq" }, - mode: params.publish_dir_mode, - pattern: "*.txt" - ], - [ - path: { "${params.outdir}/${params.aligner}/preseq/log" }, - mode: params.publish_dir_mode, - pattern: "*.log" - ] - ] - } - - withName: 'MULTIQC' { - ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } - publishDir = [ - path: { "${params.outdir}/multiqc/${params.aligner}" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - -} - - - - - - diff --git a/conf/test.config b/conf/test.config index 5b23b448..ebbab61b 100644 --- a/conf/test.config +++ b/conf/test.config @@ -1,27 +1,36 @@ /* - * ------------------------------------------------- - * Nextflow config file for running tests - * ------------------------------------------------- - * Defines bundled input files and everything required - * to run a fast and simple test. Use as follows: - * nextflow run nf-core/methylseq -profile test, - */ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running minimal tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines input files and everything required to run a fast and simple pipeline test. + + Use as follows: + nextflow run nf-core/methylseq -profile test, --outdir + +---------------------------------------------------------------------------------------- +*/ params { config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = 6.GB - max_time = 6.h - // Input data input = "${projectDir}/assets/samplesheet.csv" // Genome references - fasta = "${params.test_data_base}/reference/genome.fa" - fasta_index = "${params.test_data_base}/reference/genome.fa.fai" + fasta = "${params.pipelines_testdata_base_path}/reference/genome.fa" + fasta_index = "${params.pipelines_testdata_base_path}/reference/genome.fa.fai" +} + +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] + + withName: PRESEQ_LCEXTRAP { + errorStrategy = 'ignore' + } } -includeConfig './test_data.config' diff --git a/conf/test_data.config b/conf/test_data.config deleted file mode 100644 index ae5d5abc..00000000 --- a/conf/test_data.config +++ /dev/null @@ -1,39 +0,0 @@ -params { - // Base directory for test data - test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/methylseq" - - max_cpus = 2 - max_memory = 6.GB - max_time = 6.h - - // TODO: Add all test data to test_data.config - test_data { - 'assets' { - test_samplesheet = "${params.test_data_base}/samplesheet/samplesheet_test.csv" - } - 'workflows' { - 'methylseq' { - fasta = "${params.test_data_base}/reference/genome.fa" - fasta_index = "${params.test_data_base}/reference/genome.fa.fai" - } - } - 'sarscov2' { - 'illumina' { - test_1_fastq_gz = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz" - test_2_fastq_gz = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz" - test2_1_fastq_gz = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz" - test2_2_fastq_gz = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastq/test2_2.fastq.gz" - contigs_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fasta/contigs.fasta" - scaffolds_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fasta/scaffolds.fasta" - test_single_end_bam = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/bam/test.single_end.bam" - test_paired_end_bam = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/bam/test.paired_end.bam" - test_1_fastq_gz_fastqc_zip = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastqc/test_fastqc.zip" - } - 'genome' { - genome_fasta_gz = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta.gz" - genome_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta" - kraken2_tar_gz = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/db/kraken2.tar.gz" - } - } - } -} diff --git a/conf/test_full.config b/conf/test_full.config index f776b077..698d6234 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -15,23 +15,12 @@ params { config_profile_description = 'Full test dataset to check pipeline function' // Input data - input = "${params.test_data_base}/samplesheet/samplesheet_full.csv" + input = "${params.pipelines_testdata_base_path}/samplesheet/samplesheet_full.csv" genome = 'GRCh38' } -// ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR796/009/SRR7961089/SRR7961089_1.fastq.gz -// ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR796/009/SRR7961089/SRR7961089_2.fastq.gz -// ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR796/003/SRR7961103/SRR7961103_1.fastq.gz -// ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR796/003/SRR7961103/SRR7961103_2.fastq.gz -// ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR796/002/SRR7961102/SRR7961102_1.fastq.gz -// ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR796/002/SRR7961102/SRR7961102_2.fastq.gz -// ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR796/004/SRR7961104/SRR7961104_1.fastq.gz -// ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR796/004/SRR7961104/SRR7961104_2.fastq.gz -// ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR796/000/SRR7961150/SRR7961150_1.fastq.gz -// ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR796/000/SRR7961150/SRR7961150_2.fastq.gz -// ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR796/001/SRR7961161/SRR7961161_1.fastq.gz -// ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR796/001/SRR7961161/SRR7961161_2.fastq.gz -// ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR796/004/SRR7961164/SRR7961164_1.fastq.gz -// ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR796/004/SRR7961164/SRR7961164_2.fastq.gz -// ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR796/003/SRR7961163/SRR7961163_1.fastq.gz -// ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR796/003/SRR7961163/SRR7961163_2.fastq.gz +process { + withName: PRESEQ_LCEXTRAP { + errorStrategy = 'ignore' + } +} diff --git a/docs/images/metromap.png b/docs/images/metromap.png new file mode 100644 index 00000000..2c3912ad Binary files /dev/null and b/docs/images/metromap.png differ diff --git a/docs/images/metromap.svg b/docs/images/metromap.svg new file mode 100644 index 00000000..a6e300d7 --- /dev/null +++ b/docs/images/metromap.svg @@ -0,0 +1,123 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png deleted file mode 100755 index 361d0e47..00000000 Binary files a/docs/images/mqc_fastqc_adapter.png and /dev/null differ diff --git a/docs/images/mqc_fastqc_counts.png b/docs/images/mqc_fastqc_counts.png deleted file mode 100755 index cb39ebb8..00000000 Binary files a/docs/images/mqc_fastqc_counts.png and /dev/null differ diff --git a/docs/images/mqc_fastqc_quality.png b/docs/images/mqc_fastqc_quality.png deleted file mode 100755 index a4b89bf5..00000000 Binary files a/docs/images/mqc_fastqc_quality.png and /dev/null differ diff --git a/docs/images/nf-core-methylseq_logo_dark.png b/docs/images/nf-core-methylseq_logo_dark.png index 1f585eee..ffcd2246 100644 Binary files a/docs/images/nf-core-methylseq_logo_dark.png and b/docs/images/nf-core-methylseq_logo_dark.png differ diff --git a/docs/images/nf-core-methylseq_logo_light.png b/docs/images/nf-core-methylseq_logo_light.png index cae5ed6a..d6e00d5c 100644 Binary files a/docs/images/nf-core-methylseq_logo_light.png and b/docs/images/nf-core-methylseq_logo_light.png differ diff --git a/docs/usage.md b/docs/usage.md index 764c5940..3e376c1e 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -8,10 +8,10 @@ - [Table of contents](#table-of-contents) - [Introduction](#introduction) - - [Bismark and bwa-meth workflow](#bismark-and-bwa-meth-workflow) +- [Bismark and bwa-meth workflow](#bismark-and-bwa-meth-workflow) - [Running the pipeline](#running-the-pipeline) - - [Updating the pipeline](#updating-the-pipeline) - - [Reproducibility](#reproducibility) +- [Updating the pipeline](#updating-the-pipeline) +- [Reproducibility](#reproducibility) ## Introduction @@ -23,54 +23,14 @@ The second workflow uses [BWA-Meth](https://github.com/brentp/bwa-meth) and [Met ## Samplesheet input -You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row as shown in the examples below. +You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 4 columns, and a header row as shown in the examples below. ```bash --input '[path to samplesheet file]' ``` -### Multiple runs of the same sample - -The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes: - -```bash -sample,fastq_1,fastq_2 -CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz -CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz -CONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz -``` - -### Full samplesheet - -The pipeline will auto-detect whether a sample is single- or paired-end using the information provided in the samplesheet. The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 4 columns to match those defined in the table below. - -A final samplesheet file consisting of both single- and paired-end data may look something like the one below. This is for 6 samples, where `TREATMENT_REP3` has been sequenced twice. - -```bash -sample,fastq_1,fastq_2 -CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz -CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz -CONTROL_REP3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz -TREATMENT_REP1,AEG588A4_S4_L003_R1_001.fastq.gz, -TREATMENT_REP2,AEG588A5_S5_L003_R1_001.fastq.gz, -TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz, -TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz, -``` - -| Column | Description | -| --------- | -------------------------------------------------------------------------------------------------------------------------- | -| `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. | -| `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | -| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | - -An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. - -## Samplesheet input - -You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row as shown in the examples below. - -```bash ---input '[path to samplesheet file]' +```csv title="header.csv" +sample,fastq_1,fastq_2,genome ``` ### Multiple runs of the same sample @@ -78,10 +38,11 @@ You will need to create a samplesheet with information about the samples you wou The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes: ```csv title="samplesheet.csv" -sample,fastq_1,fastq_2 -CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz -CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz -CONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz +sample,fastq_1,fastq_2,genome +SRR389222_sub1,SRR389222_sub1.fastq.gz,, +SRR389222_sub2,SRR389222_sub2.fastq.gz,, +SRR389222_sub3,SRR389222_sub3.fastq.gz,, +Ecoli_10K_methylated,Ecoli_10K_methylated_R1.fastq.gz,Ecoli_10K_methylated_R2.fastq.gz, ``` ### Full samplesheet @@ -91,14 +52,14 @@ The pipeline will auto-detect whether a sample is single- or paired-end using th A final samplesheet file consisting of both single- and paired-end data may look something like the one below. This is for 6 samples, where `TREATMENT_REP3` has been sequenced twice. ```csv title="samplesheet.csv" -sample,fastq_1,fastq_2 -CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz -CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz -CONTROL_REP3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz -TREATMENT_REP1,AEG588A4_S4_L003_R1_001.fastq.gz, -TREATMENT_REP2,AEG588A5_S5_L003_R1_001.fastq.gz, -TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz, -TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz, +sample,fastq_1,fastq_2,genome +CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz, +CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz, +CONTROL_REP3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz, +TREATMENT_REP1,AEG588A4_S4_L003_R1_001.fastq.gz,, +TREATMENT_REP2,AEG588A5_S5_L003_R1_001.fastq.gz,, +TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz,, +TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz,, ``` | Column | Description | @@ -106,6 +67,7 @@ TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz, | `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). | | `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | | `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | +| `genome` | Reference genome to be used (OPTIONAL) | An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. @@ -142,9 +104,9 @@ The above pipeline run specified with a params file in yaml format: nextflow run nf-core/methylseq -profile docker -params-file params.yaml ``` -with `params.yaml` containing: +with: -```yaml +```yaml title="params.yaml" input: './samplesheet.csv' outdir: './results/' genome: 'GRCh37' @@ -213,6 +175,8 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) - `apptainer` - A generic configuration profile to be used with [Apptainer](https://apptainer.org/) +- `wave` + - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later). - `conda` - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. @@ -289,35 +253,35 @@ The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementatio 2. Find the latest version of the Biocontainer available on [Quay.io](https://quay.io/repository/biocontainers/pangolin?tag=latest&tab=tags) 3. Create the custom config accordingly: - - For Docker: +- For Docker: - ```nextflow - process { - withName: PANGOLIN { - container = 'quay.io/biocontainers/pangolin:3.0.5--pyhdfd78af_0' - } - } - ``` + ```nextflow + process { + withName: PANGOLIN { + container = 'quay.io/biocontainers/pangolin:3.0.5--pyhdfd78af_0' + } + } + ``` - - For Singularity: +- For Singularity: - ```nextflow - process { - withName: PANGOLIN { - container = 'https://depot.galaxyproject.org/singularity/pangolin:3.0.5--pyhdfd78af_0' - } - } - ``` + ```nextflow + process { + withName: PANGOLIN { + container = 'https://depot.galaxyproject.org/singularity/pangolin:3.0.5--pyhdfd78af_0' + } + } + ``` - - For Conda: +- For Conda: - ```nextflow - process { - withName: PANGOLIN { - conda = 'bioconda::pangolin=3.0.5' - } - } - ``` + ```nextflow + process { + withName: PANGOLIN { + conda = 'bioconda::pangolin=3.0.5' + } + } + ``` > **NB:** If you wish to periodically update individual tool-specific results (e.g. Pangolin) generated by the pipeline then you must ensure to keep the `work/` directory otherwise the `-resume` ability of the pipeline will be compromised and it will restart from scratch. @@ -329,14 +293,6 @@ See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs). -## Azure Resource Requests - -To be used with the `azurebatch` profile by specifying the `-profile azurebatch`. -We recommend providing a compute `params.vm_type` of `Standard_D16_v3` VMs by default but these options can be changed if required. - -Note that the choice of VM size depends on your quota and the overall workload during the analysis. -For a thorough list, please refer the [Azure Sizes for virtual machines in Azure](https://docs.microsoft.com/en-us/azure/virtual-machines/sizes). - ## Running in the background Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished. diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy deleted file mode 100755 index e248e4c3..00000000 --- a/lib/NfcoreTemplate.groovy +++ /dev/null @@ -1,356 +0,0 @@ -// -// This file holds several functions used within the nf-core pipeline template. -// - -import org.yaml.snakeyaml.Yaml -import groovy.json.JsonOutput -import nextflow.extension.FilesEx - -class NfcoreTemplate { - - // - // Check AWS Batch related parameters have been specified correctly - // - public static void awsBatch(workflow, params) { - if (workflow.profile.contains('awsbatch')) { - // Check params.awsqueue and params.awsregion have been set if running on AWSBatch - assert (params.awsqueue && params.awsregion) : "Specify correct --awsqueue and --awsregion parameters on AWSBatch!" - // Check outdir paths to be S3 buckets if running on AWSBatch - assert params.outdir.startsWith('s3:') : "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!" - } - } - - // - // Warn if a -profile or Nextflow config has not been provided to run the pipeline - // - public static void checkConfigProvided(workflow, log) { - if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { - log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + - "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + - " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + - " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + - " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + - "Please refer to the quick start section and usage docs for the pipeline.\n " - } - } - - // - // Generate version string - // - public static String version(workflow) { - String version_string = "" - - if (workflow.manifest.version) { - def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' - version_string += "${prefix_v}${workflow.manifest.version}" - } - - if (workflow.commitId) { - def git_shortsha = workflow.commitId.substring(0, 7) - version_string += "-g${git_shortsha}" - } - - return version_string - } - - // - // Construct and send completion email - // - public static void email(workflow, params, summary_params, projectDir, log, multiqc_report=[]) { - - // Set up the e-mail variables - def subject = "[$workflow.manifest.name] Successful: $workflow.runName" - if (!workflow.success) { - subject = "[$workflow.manifest.name] FAILED: $workflow.runName" - } - - def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] - } - - def misc_fields = [:] - misc_fields['Date Started'] = workflow.start - misc_fields['Date Completed'] = workflow.complete - misc_fields['Pipeline script file path'] = workflow.scriptFile - misc_fields['Pipeline script hash ID'] = workflow.scriptId - if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository - if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId - if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision - misc_fields['Nextflow Version'] = workflow.nextflow.version - misc_fields['Nextflow Build'] = workflow.nextflow.build - misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp - - def email_fields = [:] - email_fields['version'] = NfcoreTemplate.version(workflow) - email_fields['runName'] = workflow.runName - email_fields['success'] = workflow.success - email_fields['dateComplete'] = workflow.complete - email_fields['duration'] = workflow.duration - email_fields['exitStatus'] = workflow.exitStatus - email_fields['errorMessage'] = (workflow.errorMessage ?: 'None') - email_fields['errorReport'] = (workflow.errorReport ?: 'None') - email_fields['commandLine'] = workflow.commandLine - email_fields['projectDir'] = workflow.projectDir - email_fields['summary'] = summary << misc_fields - - // On success try attach the multiqc report - def mqc_report = null - try { - if (workflow.success) { - mqc_report = multiqc_report.getVal() - if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { - if (mqc_report.size() > 1) { - log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" - } - mqc_report = mqc_report[0] - } - } - } catch (all) { - if (multiqc_report) { - log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" - } - } - - // Check if we are only sending emails on failure - def email_address = params.email - if (!params.email && params.email_on_fail && !workflow.success) { - email_address = params.email_on_fail - } - - // Render the TXT template - def engine = new groovy.text.GStringTemplateEngine() - def tf = new File("$projectDir/assets/email_template.txt") - def txt_template = engine.createTemplate(tf).make(email_fields) - def email_txt = txt_template.toString() - - // Render the HTML template - def hf = new File("$projectDir/assets/email_template.html") - def html_template = engine.createTemplate(hf).make(email_fields) - def email_html = html_template.toString() - - // Render the sendmail template - def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit - def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] - def sf = new File("$projectDir/assets/sendmail_template.txt") - def sendmail_template = engine.createTemplate(sf).make(smail_fields) - def sendmail_html = sendmail_template.toString() - - // Send the HTML e-mail - Map colors = logColours(params.monochrome_logs) - if (email_address) { - try { - if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } - // Try to send HTML e-mail using sendmail - def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") - sendmail_tf.withWriter { w -> w << sendmail_html } - [ 'sendmail', '-t' ].execute() << sendmail_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" - } catch (all) { - // Catch failures and try with plaintext - def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] - if ( mqc_report != null && mqc_report.size() <= max_multiqc_email_size.toBytes() ) { - mail_cmd += [ '-A', mqc_report ] - } - mail_cmd.execute() << email_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" - } - } - - // Write summary e-mail HTML to a file - def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") - output_hf.withWriter { w -> w << email_html } - FilesEx.copyTo(output_hf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.html"); - output_hf.delete() - - // Write summary e-mail TXT to a file - def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") - output_tf.withWriter { w -> w << email_txt } - FilesEx.copyTo(output_tf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.txt"); - output_tf.delete() - } - - // - // Construct and send a notification to a web server as JSON - // e.g. Microsoft Teams and Slack - // - public static void IM_notification(workflow, params, summary_params, projectDir, log) { - def hook_url = params.hook_url - - def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] - } - - def misc_fields = [:] - misc_fields['start'] = workflow.start - misc_fields['complete'] = workflow.complete - misc_fields['scriptfile'] = workflow.scriptFile - misc_fields['scriptid'] = workflow.scriptId - if (workflow.repository) misc_fields['repository'] = workflow.repository - if (workflow.commitId) misc_fields['commitid'] = workflow.commitId - if (workflow.revision) misc_fields['revision'] = workflow.revision - misc_fields['nxf_version'] = workflow.nextflow.version - misc_fields['nxf_build'] = workflow.nextflow.build - misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp - - def msg_fields = [:] - msg_fields['version'] = NfcoreTemplate.version(workflow) - msg_fields['runName'] = workflow.runName - msg_fields['success'] = workflow.success - msg_fields['dateComplete'] = workflow.complete - msg_fields['duration'] = workflow.duration - msg_fields['exitStatus'] = workflow.exitStatus - msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') - msg_fields['errorReport'] = (workflow.errorReport ?: 'None') - msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") - msg_fields['projectDir'] = workflow.projectDir - msg_fields['summary'] = summary << misc_fields - - // Render the JSON template - def engine = new groovy.text.GStringTemplateEngine() - // Different JSON depending on the service provider - // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format - def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" - def hf = new File("$projectDir/assets/${json_path}") - def json_template = engine.createTemplate(hf).make(msg_fields) - def json_message = json_template.toString() - - // POST - def post = new URL(hook_url).openConnection(); - post.setRequestMethod("POST") - post.setDoOutput(true) - post.setRequestProperty("Content-Type", "application/json") - post.getOutputStream().write(json_message.getBytes("UTF-8")); - def postRC = post.getResponseCode(); - if (! postRC.equals(200)) { - log.warn(post.getErrorStream().getText()); - } - } - - // - // Dump pipeline parameters in a json file - // - public static void dump_parameters(workflow, params) { - def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') - def filename = "params_${timestamp}.json" - def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") - def jsonStr = JsonOutput.toJson(params) - temp_pf.text = JsonOutput.prettyPrint(jsonStr) - - FilesEx.copyTo(temp_pf.toPath(), "${params.outdir}/pipeline_info/params_${timestamp}.json") - temp_pf.delete() - } - - // - // Print pipeline summary on completion - // - public static void summary(workflow, params, log) { - Map colors = logColours(params.monochrome_logs) - if (workflow.success) { - if (workflow.stats.ignoredCount == 0) { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" - } - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" - } - } - - // - // ANSII Colours used for terminal logging - // - public static Map logColours(Boolean monochrome_logs) { - Map colorcodes = [:] - - // Reset / Meta - colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" - colorcodes['bold'] = monochrome_logs ? '' : "\033[1m" - colorcodes['dim'] = monochrome_logs ? '' : "\033[2m" - colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m" - colorcodes['blink'] = monochrome_logs ? '' : "\033[5m" - colorcodes['reverse'] = monochrome_logs ? '' : "\033[7m" - colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" - - // Regular Colors - colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" - colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" - colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" - colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" - colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" - colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" - colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" - colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" - - // Bold - colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" - colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" - colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" - colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" - colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" - colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" - colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" - colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" - - // Underline - colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" - colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" - colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" - colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" - colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" - colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" - colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" - colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" - - // High Intensity - colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" - colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" - colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" - colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" - colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" - colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" - colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" - colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" - - // Bold High Intensity - colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" - colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" - colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" - colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" - colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" - colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" - colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" - colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" - - return colorcodes - } - - // - // Does what is says on the tin - // - public static String dashedLine(monochrome_logs) { - Map colors = logColours(monochrome_logs) - return "-${colors.dim}----------------------------------------------------${colors.reset}-" - } - - // - // nf-core logo - // - public static String logo(workflow, monochrome_logs) { - Map colors = logColours(monochrome_logs) - String workflow_version = NfcoreTemplate.version(workflow) - String.format( - """\n - ${dashedLine(monochrome_logs)} - ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} - ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} - ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} - ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} - ${colors.green}`._,._,\'${colors.reset} - ${colors.purple} ${workflow.manifest.name} ${workflow_version}${colors.reset} - ${dashedLine(monochrome_logs)} - """.stripIndent() - ) - } -} diff --git a/lib/Utils.groovy b/lib/Utils.groovy deleted file mode 100644 index 8d030f4e..00000000 --- a/lib/Utils.groovy +++ /dev/null @@ -1,47 +0,0 @@ -// -// This file holds several Groovy functions that could be useful for any Nextflow pipeline -// - -import org.yaml.snakeyaml.Yaml - -class Utils { - - // - // When running with -profile conda, warn if channels have not been set-up appropriately - // - public static void checkCondaChannels(log) { - Yaml parser = new Yaml() - def channels = [] - try { - def config = parser.load("conda config --show channels".execute().text) - channels = config.channels - } catch(NullPointerException | IOException e) { - log.warn "Could not verify conda channel configuration." - return - } - - // Check that all channels are present - // This channel list is ordered by required channel priority. - def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] - def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean - - // Check that they are in the right order - def channel_priority_violation = false - def n = required_channels_in_order.size() - for (int i = 0; i < n - 1; i++) { - channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) - } - - if (channels_missing | channel_priority_violation) { - log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " There is a problem with your Conda configuration!\n\n" + - " You will need to set-up the conda-forge and bioconda channels correctly.\n" + - " Please refer to https://bioconda.github.io/\n" + - " The observed channel order is \n" + - " ${channels}\n" + - " but the following channel order is required:\n" + - " ${required_channels_in_order}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - } - } -} diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy deleted file mode 100755 index 0900d434..00000000 --- a/lib/WorkflowMain.groovy +++ /dev/null @@ -1,62 +0,0 @@ -// -// This file holds several functions specific to the main.nf workflow in the nf-core/methylseq pipeline -// - -import nextflow.Nextflow - -class WorkflowMain { - - // - // Citation string for pipeline - // - public static String citation(workflow) { - return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + - "* The pipeline\n" + - " https://doi.org/10.5281/zenodo.1343417\n\n" + - "* The nf-core framework\n" + - " https://doi.org/10.1038/s41587-020-0439-x\n\n" + - "* Software dependencies\n" + - " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" - } - - - // - // Validate parameters and print summary to screen - // - public static void initialise(workflow, params, log) { - - // Print workflow version and exit on --version - if (params.version) { - String workflow_version = NfcoreTemplate.version(workflow) - log.info "${workflow.manifest.name} ${workflow_version}" - System.exit(0) - } - - // Check that a -profile or Nextflow config has been provided to run the pipeline - NfcoreTemplate.checkConfigProvided(workflow, log) - - // Check that conda channels are set-up correctly - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - Utils.checkCondaChannels(log) - } - - // Check AWS batch settings - NfcoreTemplate.awsBatch(workflow, params) - - // Check input has been provided - if (!params.input) { - Nextflow.error("Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'") - } - } - // - // Get attribute from genome config file e.g. fasta - // - public static Object getGenomeAttribute(params, attribute) { - if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) { - if (params.genomes[ params.genome ].containsKey(attribute)) { - return params.genomes[ params.genome ][ attribute ] - } - } - return null - } -} diff --git a/lib/WorkflowMethylseq.groovy b/lib/WorkflowMethylseq.groovy deleted file mode 100755 index d6d5d097..00000000 --- a/lib/WorkflowMethylseq.groovy +++ /dev/null @@ -1,131 +0,0 @@ -// -// This file holds several functions specific to the workflow/methylseq.nf in the nf-core/methylseq pipeline -// - -import nextflow.Nextflow -import groovy.text.SimpleTemplateEngine - -class WorkflowMethylseq { - - // - // Check and validate parameters - // - public static void initialise(params, log) { - - genomeExistsError(params, log) - - - if (!params.fasta) { - if (!params.bismark_index || params.aligner != 'bismark') { - Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file." - } - } - } - - // - // Get workflow summary for MultiQC - // - public static String paramsSummaryMultiqc(workflow, summary) { - String summary_section = '' - for (group in summary.keySet()) { - def group_params = summary.get(group) // This gets the parameters of that particular group - if (group_params) { - summary_section += "

$group

\n" - summary_section += "
\n" - for (param in group_params.keySet()) { - summary_section += "
$param
${group_params.get(param) ?: 'N/A'}
\n" - } - summary_section += "
\n" - } - } - - String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" - yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" - yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" - yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" - yaml_file_text += "plot_type: 'html'\n" - yaml_file_text += "data: |\n" - yaml_file_text += "${summary_section}" - return yaml_file_text - } - - // - // Generate methods description for MultiQC - // - - public static String toolCitationText(params) { - - // FIXME Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", - def citation_text = [ - "Tools used in the workflow included:", - "FastQC (Andrews 2010),", - "Trim Galore! (Krueger)", - "Bismark (Krueger 2011)", - "bwa-meth (Pedersen 2014)", - "Picard (Broad Institute 2019)", - "Qualimap (Okonechnikov 2015)", - "Preseq (Daley 2013)", - "MultiQC (Ewels et al. 2016)", - "." - ].join(' ').trim() - - return citation_text - } - - public static String toolBibliographyText(params) { - - // FIXME Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "
  • Author (2023) Pub name, Journal, DOI
    • " : "", - def reference_text = [ - "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).", - "Ewels, P., Magnusson, M., Lundin, S., & KΓ€ller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354", - "https://www.bioinformatics.babraham.ac.uk/projects/trim_galore", - "Felix Krueger, Simon R. Andrews, Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications, Bioinformatics, Volume 27, Issue 11, 1 June 2011, Pages 1571–1572, doi: /10.1093/bioinformatics/btr167", - "Pedersen, Brent S. and Eyring, Kenneth and De, Subhajyoti and Yang, Ivana V. and Schwartz, David A. Fast and accurate alignment of long bisulfite-seq reads, arXiv:1401.1129, doi: 10.48550/arXiv.1401.1129", - "Picard Tools, Broad Institute. ", - "Konstantin Okonechnikov, Ana Conesa, Fernando GarcΓ­a-Alcalde, Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data, Bioinformatics, Volume 32, Issue 2, 15 January 2016, Pages 292–294, doi: 10.1093/bioinformatics/btv566", - "Daley, T., Smith, A. Predicting the molecular complexity of sequencing libraries. Nat Methods 10, 325–327 (2013). doi: 10.1038/nmeth.2375
    • ", - ].join('
  • ').trim() - - return reference_text - } - - public static String methodsDescriptionText(run_workflow, mqc_methods_yaml, params) { - // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file - def meta = [:] - meta.workflow = run_workflow.toMap() - meta["manifest_map"] = run_workflow.manifest.toMap() - - // Pipeline DOI - meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" - meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " - - // Tool references - meta["tool_citations"] = "" - meta["tool_bibliography"] = "" - - meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") - meta["tool_bibliography"] = toolBibliographyText(params) - - - def methods_text = mqc_methods_yaml.text - - def engine = new SimpleTemplateEngine() - def description_html = engine.createTemplate(methods_text).make(meta) - - return description_html - } - - // - // Exit pipeline if incorrect --genome key provided - // - private static void genomeExistsError(params, log) { - if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { - def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + - " Currently, the available genome keys are:\n" + - " ${params.genomes.keySet().join(", ")}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - Nextflow.error(error_string) - } - } -} diff --git a/lib/nfcore_external_java_deps.jar b/lib/nfcore_external_java_deps.jar deleted file mode 100644 index 805c8bb5..00000000 Binary files a/lib/nfcore_external_java_deps.jar and /dev/null differ diff --git a/main.nf b/main.nf index 4b926ef1..5c1056c8 100644 --- a/main.nf +++ b/main.nf @@ -9,70 +9,112 @@ ---------------------------------------------------------------------------------------- */ -nextflow.enable.dsl = 2 - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - GENOME PARAMETER VALUES + IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta') -params.fasta_index = WorkflowMain.getGenomeAttribute(params, 'fasta_index') -params.bismark_index = WorkflowMain.getGenomeAttribute(params, 'bismark') -params.bwa_meth_index = WorkflowMain.getGenomeAttribute(params, 'bwa_meth') +include { METHYLSEQ } from './workflows/methylseq/' +include { PREPARE_GENOME } from './subworkflows/local/prepare_genome/' +include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_methylseq_pipeline' +include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_methylseq_pipeline' +include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_methylseq_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - VALIDATE & PRINT PARAMETER SUMMARY + GENOME PARAMETER VALUES ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - -include { validateParameters; paramsHelp } from 'plugin/nf-validation' - -// Print help message if needed -if (params.help) { - def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) - def citation = '\n' + WorkflowMain.citation(workflow) + '\n' - def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" - log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs) - System.exit(0) -} - -// Validate input parameters -if (params.validate_params) { - validateParameters() -} - -WorkflowMain.initialise(workflow, params, log) +params.fasta = getGenomeAttribute('fasta') +params.fasta_index = getGenomeAttribute('fasta_index') +params.bwameth_index = getGenomeAttribute('bwameth') +params.bismark_index = params.aligner == 'bismark_hisat' ? getGenomeAttribute('bismark_hisat2') : getGenomeAttribute('bismark') /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - NAMED WORKFLOW FOR PIPELINE + NAMED WORKFLOWS FOR PIPELINE ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { METHYLSEQ } from './workflows/methylseq' - // -// WORKFLOW: Run main nf-core/methylseq analysis pipeline +// WORKFLOW: Run main analysis pipeline depending on type of input // workflow NFCORE_METHYLSEQ { - METHYLSEQ () -} + take: + samplesheet // channel: samplesheet read in from --input + + main: + + ch_versions = Channel.empty() + + // + // SUBWORKFLOW: Prepare any required reference genome indices + // + PREPARE_GENOME( + params.fasta, + params.fasta_index, + params.bismark_index, + params.bwameth_index, + ) + ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions) + + // + // WORKFLOW: Run pipeline + // + + METHYLSEQ ( + samplesheet, + ch_versions, + PREPARE_GENOME.out.fasta, + PREPARE_GENOME.out.fasta_index, + PREPARE_GENOME.out.bismark_index, + PREPARE_GENOME.out.bwameth_index, + ) + emit: + multiqc_report = METHYLSEQ.out.multiqc_report // channel: /path/to/multiqc_report.html + versions = ch_versions // channel: [version1, version2, ...] + +} /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - RUN ALL WORKFLOWS + RUN MAIN WORKFLOW ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -// -// WORKFLOW: Execute a single named workflow for the pipeline -// See: https://github.com/nf-core/rnaseq/issues/619 -// workflow { - NFCORE_METHYLSEQ () + + main: + // + // SUBWORKFLOW: Run initialisation tasks + // + PIPELINE_INITIALISATION ( + params.version, + params.validate_params, + params.monochrome_logs, + args, + params.outdir + ) + + // + // WORKFLOW: Run main workflow + // + NFCORE_METHYLSEQ ( + PIPELINE_INITIALISATION.out.samplesheet + ) + // + // SUBWORKFLOW: Run completion tasks + // + PIPELINE_COMPLETION ( + params.email, + params.email_on_fail, + params.plaintext_email, + params.outdir, + params.monochrome_logs, + params.hook_url, + NFCORE_METHYLSEQ.out.multiqc_report + ) } /* diff --git a/modules.json b/modules.json index bf351c59..53e3c295 100644 --- a/modules.json +++ b/modules.json @@ -7,135 +7,154 @@ "nf-core": { "bismark/align": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "9c4438173b1fcbf3f9004080e3af74af19d5f56e", "installed_by": ["modules"] }, "bismark/coverage2cytosine": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "430bcb24e43dabcafb5174c955300730e5ad23f7", "installed_by": ["modules"] }, "bismark/deduplicate": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "0755c617637d21b2c290b26d225debe3070aa109", "installed_by": ["modules"] }, "bismark/genomepreparation": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "3ab4739901f600a16ede0f491abfb6bf5d993cb2", "installed_by": ["modules"] }, "bismark/methylationextractor": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "0755c617637d21b2c290b26d225debe3070aa109", "installed_by": ["modules"] }, "bismark/report": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "0755c617637d21b2c290b26d225debe3070aa109", "installed_by": ["modules"] }, "bismark/summary": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "0755c617637d21b2c290b26d225debe3070aa109", "installed_by": ["modules"] }, "bwameth/align": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "9c4438173b1fcbf3f9004080e3af74af19d5f56e", "installed_by": ["modules"] }, "bwameth/index": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "a716d10039f9728f2674f45c33a95b605851ea50", "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", - "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e", + "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc", "installed_by": ["modules"] }, - "custom/dumpsoftwareversions": { + "fastqc": { "branch": "master", - "git_sha": "37dee863936732fe7e05dc598bf6e183a8e7ef73", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, - "fastqc": { + "gunzip": { "branch": "master", - "git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "methyldackel/extract": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "methyldackel/mbias": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "642a0d8afe373ac45244a7947fb8a6c0a5a312d4", + "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", "installed_by": ["modules"] }, "picard/markduplicates": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", "installed_by": ["modules"] }, "preseq/lcextrap": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc", "installed_by": ["modules"] }, "qualimap/bamqc": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "qualimap/bamqccram": { "branch": "master", - "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", "installed_by": ["modules"] }, "samtools/flagstat": { "branch": "master", - "git_sha": "570ec5bcfe19c49e16c9ca35a7a116563af6cc1c", + "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", "installed_by": ["modules"] }, "samtools/index": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", "installed_by": ["modules"] }, "samtools/sort": { "branch": "master", - "git_sha": "a0f7be95788366c1923171e358da7d049eb440f9", + "git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b", "installed_by": ["modules"] }, "samtools/stats": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", "installed_by": ["modules"] }, "trimgalore": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", "installed_by": ["modules"] }, "untar": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] } } + }, + "subworkflows": { + "nf-core": { + "utils_nextflow_pipeline": { + "branch": "master", + "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082", + "installed_by": ["subworkflows"] + }, + "utils_nfcore_pipeline": { + "branch": "master", + "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba", + "installed_by": ["subworkflows"] + }, + "utils_nfschema_plugin": { + "branch": "master", + "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c", + "installed_by": ["subworkflows"] + } + } } } } diff --git a/modules/nf-core/bismark/align/environment.yml b/modules/nf-core/bismark/align/environment.yml new file mode 100644 index 00000000..9bc4753b --- /dev/null +++ b/modules/nf-core/bismark/align/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::bismark=0.24.2 diff --git a/modules/nf-core/bismark/align/main.nf b/modules/nf-core/bismark/align/main.nf index d36f6726..d8ce3d01 100644 --- a/modules/nf-core/bismark/align/main.nf +++ b/modules/nf-core/bismark/align/main.nf @@ -2,19 +2,20 @@ process BISMARK_ALIGN { tag "$meta.id" label 'process_high' - conda "bioconda::bismark=0.24.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bismark:0.24.0--hdfd78af_0' : - 'biocontainers/bismark:0.24.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/bismark:0.24.2--hdfd78af_0' : + 'biocontainers/bismark:0.24.2--hdfd78af_0' }" input: tuple val(meta), path(reads) - path index + tuple val(meta2), path(fasta) + tuple val(meta3), path(index) output: tuple val(meta), path("*bam") , emit: bam tuple val(meta), path("*report.txt"), emit: report - tuple val(meta), path("*fq.gz") , optional:true, emit: unmapped + tuple val(meta), path("*fq.gz") , emit: unmapped, optional: true path "versions.yml" , emit: versions when: @@ -54,8 +55,11 @@ process BISMARK_ALIGN { args += " --multicore ${ccore}" } } - """ + if [ ! -f $index/$fasta ]; then + ln -s \$(readlink $fasta) $index/$fasta; + fi + bismark \\ $fastq \\ --genome $index \\ @@ -67,4 +71,17 @@ process BISMARK_ALIGN { bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bam + touch ${prefix}.report.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/bismark/align/meta.yml b/modules/nf-core/bismark/align/meta.yml index 91c17b8a..fa794b79 100644 --- a/modules/nf-core/bismark/align/meta.yml +++ b/modules/nf-core/bismark/align/meta.yml @@ -19,42 +19,74 @@ tools: documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 licence: ["GPL-3.0-or-later"] + identifier: biotools:bismark input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - index: - type: dir - description: Bismark genome index directory - pattern: "BismarkIndex" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: | + Reference genome FASTA file + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - index: + type: directory + description: Bismark genome index directory + pattern: "BismarkIndex" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" - - unmapped: - type: file - description: Output FastQ file(s) containing unmapped reads - pattern: "*.{fq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - report: - type: file - description: Bismark alignment reports - pattern: "*{report.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*report.txt": + type: file + description: Bismark alignment reports + pattern: "*{report.txt}" + - unmapped: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*fq.gz": + type: file + description: Output FastQ file(s) containing unmapped reads + pattern: "*.{fq.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" +maintainers: + - "@phue" + - "@sateeshperi" diff --git a/modules/nf-core/bismark/align/nextflow.config b/modules/nf-core/bismark/align/nextflow.config new file mode 100644 index 00000000..7e6e83b6 --- /dev/null +++ b/modules/nf-core/bismark/align/nextflow.config @@ -0,0 +1,38 @@ +process { + withName: BISMARK_ALIGN { + ext.args = { [ + params.aligner == 'bismark_hisat' ? ' --hisat2' : ' --bowtie2', + params.aligner == 'bismark_hisat' && params.known_splices ? " --known-splicesite-infile <(hisat2_extract_splice_sites.py ${known_splices})" : '', + params.pbat ? ' --pbat' : '', + ( params.single_cell || params.non_directional || params.zymo ) ? ' --non_directional' : '', + params.unmapped ? ' --unmapped' : '', + params.relax_mismatches ? " --score_min L,0,-${params.num_mismatches}" : '', + params.local_alignment ? " --local" : '', + !meta.single_end && params.minins ? " --minins ${params.minins}" : '', + meta.single_end ? '' : ( + params.maxins ? " --maxins ${params.maxins}" : ( + params.em_seq ? " --maxins 1000" : '' + ) + ) + ].join(' ').trim() } + publishDir = [ + [ + path: { "${params.outdir}/${params.aligner}/alignments/unmapped" }, + mode: params.publish_dir_mode, + pattern: "*.fq.gz", + enabled: params.unmapped + ], + [ + path: { "${params.outdir}/${params.aligner}/alignments" }, + mode: params.publish_dir_mode, + pattern: "*.bam", + enabled: (params.save_align_intermeds || params.skip_deduplication || params.rrbs) + ], + [ + path: { "${params.outdir}/${params.aligner}/alignments/logs" }, + mode: params.publish_dir_mode, + pattern: "*.txt" + ] + ] + } +} \ No newline at end of file diff --git a/modules/nf-core/bismark/align/tests/main.nf.test b/modules/nf-core/bismark/align/tests/main.nf.test new file mode 100644 index 00000000..fcd693c8 --- /dev/null +++ b/modules/nf-core/bismark/align/tests/main.nf.test @@ -0,0 +1,182 @@ +nextflow_process { + + name "Test Process BISMARK_ALIGN" + script "../main.nf" + process "BISMARK_ALIGN" + + tag "modules" + tag "modules_nfcore" + tag "bismark" + tag "bismark/align" + tag "bismark/genomepreparation" + + setup { + run("BISMARK_GENOMEPREPARATION") { + script "../../genomepreparation/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + } + + test("bowtie2 single-end / sarscov2 genome [fasta]") { + config './nextflow_bowtie2.config' + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ [ id:'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) + input[2] = BISMARK_GENOMEPREPARATION.out.index + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.bam.collect { bam(it[1]).getReadsMD5() }, + file(process.out.report[0][1]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009"), + process.out.unmapped, + process.out.versions + ).match() + } + ) + } + } + + test("bowtie2 paired-end / sarscov2 genome [fasta]") { + config './nextflow_bowtie2.config' + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = Channel.of([ [ id:'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) + input[2] = BISMARK_GENOMEPREPARATION.out.index + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.bam.collect { bam(it[1][0]).getReadsMD5() }, + file(process.out.report[0][1][0]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009"), + process.out.unmapped, + process.out.versions + ).match() + } + ) + } + } + + test("hisat2 single-end / sarscov2 genome [fasta]") { + config './nextflow_hisat2.config' + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ [ id:'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) + input[2] = BISMARK_GENOMEPREPARATION.out.index + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.bam.collect { bam(it[1]).getReadsMD5() }, + file(process.out.report[0][1]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009"), + process.out.unmapped, + process.out.versions + ).match() + } + ) + } + } + + test("hisat2 paired-end / sarscov2 genome [fasta]") { + config './nextflow_hisat2.config' + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = Channel.of([ [ id:'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) + input[2] = BISMARK_GENOMEPREPARATION.out.index + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.bam.collect { bam(it[1][0]).getReadsMD5() }, + file(process.out.report[0][1][0]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009"), + process.out.unmapped, + process.out.versions + ).match() + } + ) + } + } + + test("minimap2 single-end / sarscov2 genome [fasta]") { + config './nextflow_minimap2.config' + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ [ id:'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) + input[2] = BISMARK_GENOMEPREPARATION.out.index + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.bam.collect { bam(it[1]).getReadsMD5() }, + file(process.out.report[0][1]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5047"), + process.out.unmapped, + process.out.versions + ).match() + } + ) + } + } +} diff --git a/modules/nf-core/bismark/align/tests/main.nf.test.snap b/modules/nf-core/bismark/align/tests/main.nf.test.snap new file mode 100644 index 00000000..3842cd6d --- /dev/null +++ b/modules/nf-core/bismark/align/tests/main.nf.test.snap @@ -0,0 +1,97 @@ +{ + "bowtie2 paired-end / sarscov2 genome [fasta]": { + "content": [ + [ + "936c0d5ce713130113e99e09a5b53afd" + ], + true, + [ + + ], + [ + "versions.yml:md5,50c4bb6313fda6a7c6212ceb5dd638f5" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-13T17:35:23.192447327" + }, + "hisat2 paired-end / sarscov2 genome [fasta]": { + "content": [ + [ + "936c0d5ce713130113e99e09a5b53afd" + ], + true, + [ + + ], + [ + "versions.yml:md5,50c4bb6313fda6a7c6212ceb5dd638f5" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-13T17:36:10.145541495" + }, + "minimap2 single-end / sarscov2 genome [fasta]": { + "content": [ + [ + "d354e6c6d6a06e36630590de8f27031a" + ], + true, + [ + + ], + [ + "versions.yml:md5,50c4bb6313fda6a7c6212ceb5dd638f5" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-13T17:36:32.094369612" + }, + "bowtie2 single-end / sarscov2 genome [fasta]": { + "content": [ + [ + "936c0d5ce713130113e99e09a5b53afd" + ], + true, + [ + + ], + [ + "versions.yml:md5,50c4bb6313fda6a7c6212ceb5dd638f5" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-13T17:34:58.431003479" + }, + "hisat2 single-end / sarscov2 genome [fasta]": { + "content": [ + [ + "936c0d5ce713130113e99e09a5b53afd" + ], + true, + [ + + ], + [ + "versions.yml:md5,50c4bb6313fda6a7c6212ceb5dd638f5" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-13T17:35:45.557280528" + } +} \ No newline at end of file diff --git a/modules/nf-core/bismark/align/tests/nextflow_bowtie2.config b/modules/nf-core/bismark/align/tests/nextflow_bowtie2.config new file mode 100644 index 00000000..cf0357e2 --- /dev/null +++ b/modules/nf-core/bismark/align/tests/nextflow_bowtie2.config @@ -0,0 +1,8 @@ +process { + withName: BISMARK_ALIGN { + ext.args = '--bowtie2' + } + withName: BISMARK_GENOMEPREPARATION { + ext.args = '--bowtie2' + } +} \ No newline at end of file diff --git a/modules/nf-core/bismark/align/tests/nextflow_hisat2.config b/modules/nf-core/bismark/align/tests/nextflow_hisat2.config new file mode 100644 index 00000000..5b962ae0 --- /dev/null +++ b/modules/nf-core/bismark/align/tests/nextflow_hisat2.config @@ -0,0 +1,8 @@ +process { + withName: BISMARK_ALIGN { + ext.args = '--hisat2' + } + withName: BISMARK_GENOMEPREPARATION { + ext.args = '--hisat2' + } +} \ No newline at end of file diff --git a/modules/nf-core/bismark/align/tests/nextflow_minimap2.config b/modules/nf-core/bismark/align/tests/nextflow_minimap2.config new file mode 100644 index 00000000..dd46fe26 --- /dev/null +++ b/modules/nf-core/bismark/align/tests/nextflow_minimap2.config @@ -0,0 +1,8 @@ +process { + withName: BISMARK_ALIGN { + ext.args = '--minimap2' + } + withName: BISMARK_GENOMEPREPARATION { + ext.args = '--minimap2' + } +} \ No newline at end of file diff --git a/modules/nf-core/bismark/coverage2cytosine/environment.yml b/modules/nf-core/bismark/coverage2cytosine/environment.yml new file mode 100644 index 00000000..9bc4753b --- /dev/null +++ b/modules/nf-core/bismark/coverage2cytosine/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::bismark=0.24.2 diff --git a/modules/nf-core/bismark/coverage2cytosine/main.nf b/modules/nf-core/bismark/coverage2cytosine/main.nf index f5429700..fe65c658 100644 --- a/modules/nf-core/bismark/coverage2cytosine/main.nf +++ b/modules/nf-core/bismark/coverage2cytosine/main.nf @@ -2,17 +2,18 @@ process BISMARK_COVERAGE2CYTOSINE { tag "$meta.id" label 'process_low' - conda "bioconda::bismark=0.23.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bismark:0.24.0--hdfd78af_0' : - 'biocontainers/bismark:0.24.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/bismark:0.24.2--hdfd78af_0' : + 'biocontainers/bismark:0.24.2--hdfd78af_0' }" input: tuple val(meta), path(coverage_file) - path index + tuple val(meta2), path(fasta) + tuple val(meta3), path(index) output: - tuple val(meta), path("*.cov.gz"), optional: true , emit: coverage + tuple val(meta), path("*.cov.gz") , emit: coverage, optional: true tuple val(meta), path("*report.txt.gz") , emit: report tuple val(meta), path("*cytosine_context_summary.txt") , emit: summary path "versions.yml" , emit: versions @@ -23,8 +24,11 @@ process BISMARK_COVERAGE2CYTOSINE { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - """ + if [ ! -f $index/$fasta ]; then + ln -s \$(readlink $fasta) $index/$fasta; + fi + coverage2cytosine \\ $coverage_file \\ --genome $index \\ @@ -37,4 +41,18 @@ process BISMARK_COVERAGE2CYTOSINE { bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.cov.gz + touch ${prefix}.report.txt.gz + touch ${prefix}.cytosine_context_summary.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/bismark/coverage2cytosine/meta.yml b/modules/nf-core/bismark/coverage2cytosine/meta.yml index 511578c8..705b57f5 100644 --- a/modules/nf-core/bismark/coverage2cytosine/meta.yml +++ b/modules/nf-core/bismark/coverage2cytosine/meta.yml @@ -20,44 +20,73 @@ tools: documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 licence: ["GPL-3.0-or-later"] - + identifier: biotools:bismark input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - coverage_file: - type: file - description: | - A file containing methylation calls per position, in the format produced by bismark_methylation_extractor. - - index: - type: dir - description: Bismark genome index directory - pattern: "BismarkIndex" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - coverage_file: + type: file + description: | + A file containing methylation calls per position, in the format produced by bismark_methylation_extractor. + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: | + Reference genome FASTA file + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - index: + type: directory + description: Bismark genome index directory + pattern: "BismarkIndex" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - coverage: - type: file - description: A file containing methylation calls per position. - pattern: "*.cov.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cov.gz": + type: file + description: A file containing methylation calls per position. + pattern: "*.cov.gz" - report: - type: file - description: Genomic cytosine context results. - pattern: "*report.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*report.txt.gz": + type: file + description: Genomic cytosine context results. + pattern: "*report.txt.gz" - summary: - type: file - description: Cyotosine context summary report. - pattern: "*cytosine_context_summary.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*cytosine_context_summary.txt": + type: file + description: Cyotosine context summary report. + pattern: "*cytosine_context_summary.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ewels" +maintainers: + - "@ewels" + - "@sateeshperi" diff --git a/modules/nf-core/bismark/coverage2cytosine/nextflow.config b/modules/nf-core/bismark/coverage2cytosine/nextflow.config new file mode 100644 index 00000000..f593a1d1 --- /dev/null +++ b/modules/nf-core/bismark/coverage2cytosine/nextflow.config @@ -0,0 +1,20 @@ +process { + withName: BISMARK_COVERAGE2CYTOSINE { + ext.args = params.nomeseq ? '--nome-seq' : '' + publishDir = [ + path: { "${params.outdir}/bismark/coverage2cytosine/summaries" }, + mode: params.publish_dir_mode, + pattern: "*_summary.txt" + ] + publishDir = [ + path: { "${params.outdir}/bismark/coverage2cytosine/reports" }, + mode: params.publish_dir_mode, + pattern: "*_report.txt.gz" + ] + publishDir = [ + path: { "${params.outdir}/bismark/coverage2cytosine/coverage" }, + mode: params.publish_dir_mode, + pattern: "*cov.gz" + ] + } +} \ No newline at end of file diff --git a/modules/nf-core/bismark/coverage2cytosine/tests/main.nf.test b/modules/nf-core/bismark/coverage2cytosine/tests/main.nf.test new file mode 100644 index 00000000..ac4f7ae2 --- /dev/null +++ b/modules/nf-core/bismark/coverage2cytosine/tests/main.nf.test @@ -0,0 +1,62 @@ +nextflow_process { + + name "Test Process BISMARK_COVERAGE2CYTOSINE" + script "../main.nf" + process "BISMARK_COVERAGE2CYTOSINE" + + tag "modules" + tag "modules_nfcore" + tag "bismark" + tag "bismark/coverage2cytosine" + tag "bismark/methylationextractor" + tag "bismark/genomepreparation" + + test("sarscov2 genome [fasta] | sarscov2 paired-end methylated [bam]") { + + setup { + run("BISMARK_GENOMEPREPARATION") { + script "../../genomepreparation/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + run("BISMARK_METHYLATIONEXTRACTOR") { + script "../../methylationextractor/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.bam', checkIfExists: true) + ]) + input[1] = BISMARK_GENOMEPREPARATION.out.index + """ + } + } + } + + when { + process { + """ + input[0] = BISMARK_METHYLATIONEXTRACTOR.out.coverage + input[1] = input[1] = Channel.of([ [ id:'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) + input[2] = BISMARK_GENOMEPREPARATION.out.index + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/bismark/coverage2cytosine/tests/main.nf.test.snap b/modules/nf-core/bismark/coverage2cytosine/tests/main.nf.test.snap new file mode 100644 index 00000000..58c02986 --- /dev/null +++ b/modules/nf-core/bismark/coverage2cytosine/tests/main.nf.test.snap @@ -0,0 +1,61 @@ +{ + "sarscov2 genome [fasta] | sarscov2 paired-end methylated [bam]": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.CpG_report.txt.gz:md5,0b83c760c7b3df21a320f054bbb865fb" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cytosine_context_summary.txt:md5,5ed486bfa844a5e476a7ab054a7a8d6b" + ] + ], + "3": [ + "versions.yml:md5,d68e9a778e9c156a80869e880c0518c8" + ], + "coverage": [ + + ], + "report": [ + [ + { + "id": "test", + "single_end": false + }, + "test.CpG_report.txt.gz:md5,0b83c760c7b3df21a320f054bbb865fb" + ] + ], + "summary": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cytosine_context_summary.txt:md5,5ed486bfa844a5e476a7ab054a7a8d6b" + ] + ], + "versions": [ + "versions.yml:md5,d68e9a778e9c156a80869e880c0518c8" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-13T18:20:45.406703493" + } +} \ No newline at end of file diff --git a/modules/nf-core/bismark/deduplicate/environment.yml b/modules/nf-core/bismark/deduplicate/environment.yml new file mode 100644 index 00000000..9bc4753b --- /dev/null +++ b/modules/nf-core/bismark/deduplicate/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::bismark=0.24.2 diff --git a/modules/nf-core/bismark/deduplicate/main.nf b/modules/nf-core/bismark/deduplicate/main.nf index 7e238d77..2da9312c 100644 --- a/modules/nf-core/bismark/deduplicate/main.nf +++ b/modules/nf-core/bismark/deduplicate/main.nf @@ -2,10 +2,10 @@ process BISMARK_DEDUPLICATE { tag "$meta.id" label 'process_high' - conda "bioconda::bismark=0.24.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bismark:0.24.0--hdfd78af_0' : - 'biocontainers/bismark:0.24.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/bismark:0.24.2--hdfd78af_0' : + 'biocontainers/bismark:0.24.2--hdfd78af_0' }" input: tuple val(meta), path(bam) @@ -19,9 +19,9 @@ process BISMARK_DEDUPLICATE { task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def seqtype = meta.single_end ? '-s' : '-p' + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def seqtype = meta.single_end ? '-s' : '-p' """ deduplicate_bismark \\ $args \\ @@ -33,4 +33,17 @@ process BISMARK_DEDUPLICATE { bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.deduplicated.bam + touch ${prefix}.deduplication_report.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/bismark/deduplicate/meta.yml b/modules/nf-core/bismark/deduplicate/meta.yml index a310a851..5de7c210 100644 --- a/modules/nf-core/bismark/deduplicate/meta.yml +++ b/modules/nf-core/bismark/deduplicate/meta.yml @@ -21,33 +21,45 @@ tools: documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 licence: ["GPL-3.0-or-later"] + identifier: biotools:bismark input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file containing read alignments - pattern: "*.{bam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file containing read alignments + pattern: "*.{bam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Deduplicated output BAM file containing read alignments - pattern: "*.{deduplicated.bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.deduplicated.bam": + type: file + description: Deduplicated output BAM file containing read alignments + pattern: "*.{deduplicated.bam}" - report: - type: file - description: Bismark deduplication reports - pattern: "*.{deduplication_report.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.deduplication_report.txt": + type: file + description: Bismark deduplication reports + pattern: "*.{deduplication_report.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" +maintainers: + - "@phue" + - "@sateeshperi" diff --git a/modules/nf-core/bismark/deduplicate/nextflow.config b/modules/nf-core/bismark/deduplicate/nextflow.config new file mode 100644 index 00000000..b2b51c29 --- /dev/null +++ b/modules/nf-core/bismark/deduplicate/nextflow.config @@ -0,0 +1,12 @@ +process { + withName: BISMARK_DEDUPLICATE { + ext.args = '' + publishDir = [ + [ + path: { "${params.outdir}/${params.aligner}/deduplicated/logs" }, + mode: params.publish_dir_mode, + pattern: "*.txt" + ] + ] + } +} \ No newline at end of file diff --git a/modules/nf-core/bismark/deduplicate/tests/main.nf.test b/modules/nf-core/bismark/deduplicate/tests/main.nf.test new file mode 100644 index 00000000..a82b4b73 --- /dev/null +++ b/modules/nf-core/bismark/deduplicate/tests/main.nf.test @@ -0,0 +1,39 @@ +nextflow_process { + + name "Test Process BISMARK_DEDUPLICATE" + script "../main.nf" + process "BISMARK_DEDUPLICATE" + + tag "bismark" + tag "bismark/deduplicate" + tag "modules" + tag "modules_nfcore" + + test("sarscov2 paired-end methylated [bam]") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.bam.collect { bam(it[1]).getReadsMD5() }, + process.out.report, + process.out.versions + ).match() + } + ) + } + + } + +} diff --git a/modules/nf-core/bismark/deduplicate/tests/main.nf.test.snap b/modules/nf-core/bismark/deduplicate/tests/main.nf.test.snap new file mode 100644 index 00000000..98e72559 --- /dev/null +++ b/modules/nf-core/bismark/deduplicate/tests/main.nf.test.snap @@ -0,0 +1,26 @@ +{ + "sarscov2 paired-end methylated [bam]": { + "content": [ + [ + "8036b4b920354438ddd1871c88f5088" + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.methylated.deduplication_report.txt:md5,86aaf87bac9ccdc3cc83628f20b902dc" + ] + ], + [ + "versions.yml:md5,80ac07cad7c9ea075ffd7b75d74c39cd" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-13T18:31:09.804719461" + } +} \ No newline at end of file diff --git a/modules/nf-core/bismark/genomepreparation/environment.yml b/modules/nf-core/bismark/genomepreparation/environment.yml new file mode 100644 index 00000000..9bc4753b --- /dev/null +++ b/modules/nf-core/bismark/genomepreparation/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::bismark=0.24.2 diff --git a/modules/nf-core/bismark/genomepreparation/main.nf b/modules/nf-core/bismark/genomepreparation/main.nf index 8f424443..c94e9fec 100644 --- a/modules/nf-core/bismark/genomepreparation/main.nf +++ b/modules/nf-core/bismark/genomepreparation/main.nf @@ -2,17 +2,17 @@ process BISMARK_GENOMEPREPARATION { tag "$fasta" label 'process_high' - conda "bioconda::bismark=0.24.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bismark:0.24.0--hdfd78af_0' : - 'biocontainers/bismark:0.24.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/bismark:0.24.2--hdfd78af_0' : + 'biocontainers/bismark:0.24.2--hdfd78af_0' }" input: - path fasta, stageAs: "BismarkIndex/*" + tuple val(meta), path(fasta, name:"BismarkIndex/") output: - path "BismarkIndex" , emit: index - path "versions.yml" , emit: versions + tuple val(meta), path("BismarkIndex"), emit: index + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -24,6 +24,37 @@ process BISMARK_GENOMEPREPARATION { $args \\ BismarkIndex + rm $fasta + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + """ + rm $fasta + + mkdir -p BismarkIndex/Bisulfite_Genome/CT_conversion + touch BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.1.bt2 + touch BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.2.bt2 + touch BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.3.bt2 + touch BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.4.bt2 + touch BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.rev.1.bt2 + touch BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.rev.2.bt2 + touch BismarkIndex/Bisulfite_Genome/CT_conversion/genome_mfa.CT_conversion.fa + + mkdir -p BismarkIndex/Bisulfite_Genome/GA_conversion + touch BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.1.bt2 + touch BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.2.bt2 + touch BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.3.bt2 + touch BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.4.bt2 + touch BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.rev.1.bt2 + touch BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.rev.2.bt2 + touch BismarkIndex/Bisulfite_Genome/GA_conversion/genome_mfa.GA_conversion.fa + cat <<-END_VERSIONS > versions.yml "${task.process}": bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') diff --git a/modules/nf-core/bismark/genomepreparation/meta.yml b/modules/nf-core/bismark/genomepreparation/meta.yml index 23588e1d..c1880271 100644 --- a/modules/nf-core/bismark/genomepreparation/meta.yml +++ b/modules/nf-core/bismark/genomepreparation/meta.yml @@ -21,18 +21,34 @@ tools: documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 licence: ["GPL-3.0-or-later"] + identifier: biotools:bismark input: - - fasta: - type: file - description: Input genome fasta file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file output: - index: - type: dir - description: Bismark genome index directory - pattern: "BismarkIndex" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - BismarkIndex: + type: directory + description: Bismark genome index directory + pattern: "BismarkIndex" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" +maintainers: + - "@phue" + - "@sateeshperi" diff --git a/modules/nf-core/bismark/genomepreparation/nextflow.config b/modules/nf-core/bismark/genomepreparation/nextflow.config new file mode 100644 index 00000000..ed506125 --- /dev/null +++ b/modules/nf-core/bismark/genomepreparation/nextflow.config @@ -0,0 +1,14 @@ +process { + withName: BISMARK_GENOMEPREPARATION { + ext.args = [ + params.aligner == 'bismark_hisat' ? ' --hisat2' : ' --bowtie2', + params.slamseq ? ' --slam' : '' + ].join(' ').trim() + publishDir = [ + path: { "${params.outdir}/${params.aligner}/reference_genome" }, + saveAs: { it =~ /.*\.yml/ ? null : it }, + mode: params.publish_dir_mode, + enabled: params.save_reference + ] + } +} \ No newline at end of file diff --git a/modules/nf-core/bismark/genomepreparation/tests/main.nf.test b/modules/nf-core/bismark/genomepreparation/tests/main.nf.test new file mode 100644 index 00000000..3ba99722 --- /dev/null +++ b/modules/nf-core/bismark/genomepreparation/tests/main.nf.test @@ -0,0 +1,56 @@ +nextflow_process { + + name "Test Process BISMARK_GENOMEPREPARATION" + script "../main.nf" + process "BISMARK_GENOMEPREPARATION" + + tag "modules" + tag "bismark/genomepreparation" + tag "bismark" + tag "modules_nfcore" + + test("sarscov2 genome [fasta]") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 genome [fasta] - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap b/modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap new file mode 100644 index 00000000..d56b414d --- /dev/null +++ b/modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap @@ -0,0 +1,152 @@ +{ + "sarscov2 genome [fasta] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + [ + [ + "BS_CT.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_CT.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_CT.3.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_CT.4.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_CT.rev.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_CT.rev.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome_mfa.CT_conversion.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + "BS_GA.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_GA.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_GA.3.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_GA.4.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_GA.rev.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_GA.rev.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome_mfa.GA_conversion.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ] + ] + ], + "1": [ + "versions.yml:md5,4d9a42530334575b18a6bde4ae72f7d6" + ], + "index": [ + [ + { + "id": "test" + }, + [ + [ + [ + "BS_CT.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_CT.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_CT.3.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_CT.4.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_CT.rev.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_CT.rev.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome_mfa.CT_conversion.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + "BS_GA.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_GA.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_GA.3.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_GA.4.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_GA.rev.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "BS_GA.rev.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome_mfa.GA_conversion.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ] + ] + ], + "versions": [ + "versions.yml:md5,4d9a42530334575b18a6bde4ae72f7d6" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T15:50:44.009733" + }, + "sarscov2 genome [fasta]": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + [ + [ + "BS_CT.1.bt2:md5,10a8854e5eeb95629f46d24b0d8da70c", + "BS_CT.2.bt2:md5,bc5d407e6fce3e1cdb4b23ab2a20f707", + "BS_CT.3.bt2:md5,4ed93abba181d8dfab2e303e33114777", + "BS_CT.4.bt2:md5,6c4f549575e5882ff3a97ae10ae2e7be", + "BS_CT.rev.1.bt2:md5,d37d586b41b6a36efb25839961d242cb", + "BS_CT.rev.2.bt2:md5,48bf400de85cd7324fbf6bf38fe2dc95", + "genome_mfa.CT_conversion.fa:md5,903b9f357eea4a5f36e21e78e0fe1dfa" + ], + [ + "BS_GA.1.bt2:md5,a6fa4068ed10872568f32568c66cb600", + "BS_GA.2.bt2:md5,fc5b634e2f5137801e3801d62ad05f74", + "BS_GA.3.bt2:md5,4ed93abba181d8dfab2e303e33114777", + "BS_GA.4.bt2:md5,b1e855685ed634daa7df8e180c9b2fc4", + "BS_GA.rev.1.bt2:md5,17f51e65f44477962226a83b369b2bc4", + "BS_GA.rev.2.bt2:md5,d36044c5dfe37af0411f60d446585bc6", + "genome_mfa.GA_conversion.fa:md5,e529375ec2039112161465b5169fcd59" + ] + ] + ] + ] + ], + "1": [ + "versions.yml:md5,4d9a42530334575b18a6bde4ae72f7d6" + ], + "index": [ + [ + { + "id": "test" + }, + [ + [ + [ + "BS_CT.1.bt2:md5,10a8854e5eeb95629f46d24b0d8da70c", + "BS_CT.2.bt2:md5,bc5d407e6fce3e1cdb4b23ab2a20f707", + "BS_CT.3.bt2:md5,4ed93abba181d8dfab2e303e33114777", + "BS_CT.4.bt2:md5,6c4f549575e5882ff3a97ae10ae2e7be", + "BS_CT.rev.1.bt2:md5,d37d586b41b6a36efb25839961d242cb", + "BS_CT.rev.2.bt2:md5,48bf400de85cd7324fbf6bf38fe2dc95", + "genome_mfa.CT_conversion.fa:md5,903b9f357eea4a5f36e21e78e0fe1dfa" + ], + [ + "BS_GA.1.bt2:md5,a6fa4068ed10872568f32568c66cb600", + "BS_GA.2.bt2:md5,fc5b634e2f5137801e3801d62ad05f74", + "BS_GA.3.bt2:md5,4ed93abba181d8dfab2e303e33114777", + "BS_GA.4.bt2:md5,b1e855685ed634daa7df8e180c9b2fc4", + "BS_GA.rev.1.bt2:md5,17f51e65f44477962226a83b369b2bc4", + "BS_GA.rev.2.bt2:md5,d36044c5dfe37af0411f60d446585bc6", + "genome_mfa.GA_conversion.fa:md5,e529375ec2039112161465b5169fcd59" + ] + ] + ] + ] + ], + "versions": [ + "versions.yml:md5,4d9a42530334575b18a6bde4ae72f7d6" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-13T08:26:20.352083082" + } +} \ No newline at end of file diff --git a/modules/nf-core/bismark/methylationextractor/environment.yml b/modules/nf-core/bismark/methylationextractor/environment.yml new file mode 100644 index 00000000..9bc4753b --- /dev/null +++ b/modules/nf-core/bismark/methylationextractor/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::bismark=0.24.2 diff --git a/modules/nf-core/bismark/methylationextractor/main.nf b/modules/nf-core/bismark/methylationextractor/main.nf index 2a3e5d22..3a71d35d 100644 --- a/modules/nf-core/bismark/methylationextractor/main.nf +++ b/modules/nf-core/bismark/methylationextractor/main.nf @@ -2,14 +2,14 @@ process BISMARK_METHYLATIONEXTRACTOR { tag "$meta.id" label 'process_high' - conda "bioconda::bismark=0.24.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bismark:0.24.0--hdfd78af_0' : - 'biocontainers/bismark:0.24.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/bismark:0.24.2--hdfd78af_0' : + 'biocontainers/bismark:0.24.2--hdfd78af_0' }" input: tuple val(meta), path(bam) - path index + tuple val(meta2), path(index) output: tuple val(meta), path("*.bedGraph.gz") , emit: bedgraph @@ -49,4 +49,20 @@ process BISMARK_METHYLATIONEXTRACTOR { bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bedGraph.gz + touch ${prefix}.txt.gz + touch ${prefix}.cov.gz + touch ${prefix}_splitting_report.txt + touch ${prefix}.M-bias.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/bismark/methylationextractor/meta.yml b/modules/nf-core/bismark/methylationextractor/meta.yml index 81b14144..2aaefdfa 100644 --- a/modules/nf-core/bismark/methylationextractor/meta.yml +++ b/modules/nf-core/bismark/methylationextractor/meta.yml @@ -20,49 +20,84 @@ tools: documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 licence: ["GPL-3.0-or-later"] + identifier: biotools:bismark input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file containing read alignments - pattern: "*.{bam}" - - index: - type: dir - description: Bismark genome index directory - pattern: "BismarkIndex" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file containing read alignments + pattern: "*.{bam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - index: + type: directory + description: Bismark genome index directory + pattern: "BismarkIndex" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bedgraph: - type: file - description: Bismark output file containing coverage and methylation metrics - pattern: "*.{bedGraph.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bedGraph.gz": + type: file + description: Bismark output file containing coverage and methylation metrics + pattern: "*.{bedGraph.gz}" - methylation_calls: - type: file - description: Bismark output file containing strand-specific methylation calls - pattern: "*.{txt.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt.gz": + type: file + description: Bismark output file containing strand-specific methylation calls + pattern: "*.{txt.gz}" - coverage: - type: file - description: Bismark output file containing coverage metrics - pattern: "*.{cov.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cov.gz": + type: file + description: Bismark output file containing coverage metrics + pattern: "*.{cov.gz}" - report: - type: file - description: Bismark splitting reports - pattern: "*_{splitting_report.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_splitting_report.txt": + type: file + description: Bismark splitting reports + pattern: "*_{splitting_report.txt}" - mbias: - type: file - description: Text file containing methylation bias information - pattern: "*.{M-bias.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.M-bias.txt": + type: file + description: Text file containing methylation bias information + pattern: "*.{M-bias.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" +maintainers: + - "@phue" + - "@sateeshperi" diff --git a/modules/nf-core/bismark/methylationextractor/nextflow.config b/modules/nf-core/bismark/methylationextractor/nextflow.config new file mode 100644 index 00000000..b312885b --- /dev/null +++ b/modules/nf-core/bismark/methylationextractor/nextflow.config @@ -0,0 +1,41 @@ +process { + withName: BISMARK_METHYLATIONEXTRACTOR { + ext.args = { [ + params.comprehensive ? ' --comprehensive --merge_non_CpG' : '', + params.meth_cutoff ? " --cutoff ${params.meth_cutoff}" : '', + params.nomeseq ? '--CX' : '', + params.ignore_r1 > 0 ? "--ignore ${params.ignore_r1}" : '', + params.ignore_3prime_r1 > 0 ? "--ignore_3prime ${params.ignore_3prime_r1}" : '', + meta.single_end ? '' : (params.no_overlap ? ' --no_overlap' : '--include_overlap'), + meta.single_end ? '' : (params.ignore_r2 > 0 ? "--ignore_r2 ${params.ignore_r2}" : ""), + meta.single_end ? '' : (params.ignore_3prime_r2 > 0 ? "--ignore_3prime_r2 ${params.ignore_3prime_r2}": "") + ].join(' ').trim() } + publishDir = [ + [ + path: { "${params.outdir}/${params.aligner}/methylation_calls/mbias" }, + mode: params.publish_dir_mode, + pattern: "*M-bias.txt" + ], + [ + path: { "${params.outdir}/${params.aligner}/methylation_calls/methylation_coverage" }, + mode: params.publish_dir_mode, + pattern: "*cov.gz" + ], + [ + path: { "${params.outdir}/${params.aligner}/methylation_calls/bedGraph" }, + mode: params.publish_dir_mode, + pattern: "*bedGraph.gz" + ], + [ + path: { "${params.outdir}/${params.aligner}/methylation_calls/splitting_report" }, + mode: params.publish_dir_mode, + pattern: "*splitting_report.txt" + ], + [ + path: { "${params.outdir}/${params.aligner}/methylation_calls/methylation_calls" }, + mode: params.publish_dir_mode, + pattern: "*txt.gz" + ] + ] + } +} \ No newline at end of file diff --git a/modules/nf-core/bismark/methylationextractor/tests/main.nf.test b/modules/nf-core/bismark/methylationextractor/tests/main.nf.test new file mode 100644 index 00000000..fce2e35b --- /dev/null +++ b/modules/nf-core/bismark/methylationextractor/tests/main.nf.test @@ -0,0 +1,50 @@ +nextflow_process { + + name "Test Process BISMARK_METHYLATIONEXTRACTOR" + script "../main.nf" + process "BISMARK_METHYLATIONEXTRACTOR" + + tag "modules" + tag "modules_nfcore" + tag "bismark" + tag "bismark/methylationextractor" + tag "bismark/genomepreparation" + + test("sarscov2 paired-end methylated [bam] / sarscov2 genome [fasta]") { + + setup { + run("BISMARK_GENOMEPREPARATION") { + script "../../genomepreparation/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.bam', checkIfExists: true) + ]) + input[1] = BISMARK_GENOMEPREPARATION.out.index + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match()} + ) + } + + } + +} diff --git a/modules/nf-core/bismark/methylationextractor/tests/main.nf.test.snap b/modules/nf-core/bismark/methylationextractor/tests/main.nf.test.snap new file mode 100644 index 00000000..dd83c755 --- /dev/null +++ b/modules/nf-core/bismark/methylationextractor/tests/main.nf.test.snap @@ -0,0 +1,123 @@ +{ + "sarscov2 paired-end methylated [bam] / sarscov2 genome [fasta]": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.methylated.bedGraph.gz:md5,3e461daa0b89ee4eeb76e336ad6aad7a" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "CHG_OB_test.paired_end.methylated.txt.gz:md5,de98c596d927732d0a5a4cf4b3b9e7ae", + "CHG_OT_test.paired_end.methylated.txt.gz:md5,64ea7598db55ae810bc6846afe1941b8", + "CHH_OB_test.paired_end.methylated.txt.gz:md5,fac33b1186436430913d844662862972", + "CHH_OT_test.paired_end.methylated.txt.gz:md5,2a1509bd87032f9ae2c7ca5d0d728b3a", + "CpG_OB_test.paired_end.methylated.txt.gz:md5,dfecc0ceaca41ac848ff7d6e990a3f17", + "CpG_OT_test.paired_end.methylated.txt.gz:md5,5280f3ea983ee0f33b7c467f63f6c6d1" + ] + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.methylated.bismark.cov.gz:md5,1524da1472ed1ad0c0663a9676c142e0" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.methylated_splitting_report.txt:md5,25f4f2fbf35cc9d7dc9e21209c40ca07" + ] + ], + "4": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.methylated.M-bias.txt:md5,0b100924d46b3c35115f1206f34c4a59" + ] + ], + "5": [ + "versions.yml:md5,c01f97c8def49098023fded456717776" + ], + "bedgraph": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.methylated.bedGraph.gz:md5,3e461daa0b89ee4eeb76e336ad6aad7a" + ] + ], + "coverage": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.methylated.bismark.cov.gz:md5,1524da1472ed1ad0c0663a9676c142e0" + ] + ], + "mbias": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.methylated.M-bias.txt:md5,0b100924d46b3c35115f1206f34c4a59" + ] + ], + "methylation_calls": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "CHG_OB_test.paired_end.methylated.txt.gz:md5,de98c596d927732d0a5a4cf4b3b9e7ae", + "CHG_OT_test.paired_end.methylated.txt.gz:md5,64ea7598db55ae810bc6846afe1941b8", + "CHH_OB_test.paired_end.methylated.txt.gz:md5,fac33b1186436430913d844662862972", + "CHH_OT_test.paired_end.methylated.txt.gz:md5,2a1509bd87032f9ae2c7ca5d0d728b3a", + "CpG_OB_test.paired_end.methylated.txt.gz:md5,dfecc0ceaca41ac848ff7d6e990a3f17", + "CpG_OT_test.paired_end.methylated.txt.gz:md5,5280f3ea983ee0f33b7c467f63f6c6d1" + ] + ] + ], + "report": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.methylated_splitting_report.txt:md5,25f4f2fbf35cc9d7dc9e21209c40ca07" + ] + ], + "versions": [ + "versions.yml:md5,c01f97c8def49098023fded456717776" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-13T18:09:13.593807534" + } +} \ No newline at end of file diff --git a/modules/nf-core/bismark/report/environment.yml b/modules/nf-core/bismark/report/environment.yml new file mode 100644 index 00000000..9bc4753b --- /dev/null +++ b/modules/nf-core/bismark/report/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::bismark=0.24.2 diff --git a/modules/nf-core/bismark/report/main.nf b/modules/nf-core/bismark/report/main.nf index 804a141d..e68ee8e5 100644 --- a/modules/nf-core/bismark/report/main.nf +++ b/modules/nf-core/bismark/report/main.nf @@ -2,10 +2,10 @@ process BISMARK_REPORT { tag "$meta.id" label 'process_low' - conda "bioconda::bismark=0.24.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bismark:0.24.0--hdfd78af_0' : - 'biocontainers/bismark:0.24.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/bismark:0.24.2--hdfd78af_0' : + 'biocontainers/bismark:0.24.2--hdfd78af_0' }" input: tuple val(meta), path(align_report), path(dedup_report), path(splitting_report), path(mbias) @@ -27,4 +27,17 @@ process BISMARK_REPORT { bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.report.txt + touch ${prefix}.report.html + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/bismark/report/meta.yml b/modules/nf-core/bismark/report/meta.yml index 1f6be782..c1191e9b 100644 --- a/modules/nf-core/bismark/report/meta.yml +++ b/modules/nf-core/bismark/report/meta.yml @@ -18,44 +18,47 @@ tools: documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 licence: ["GPL-3.0-or-later"] + identifier: biotools:bismark input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - align_report: - type: file - description: Bismark alignment reports - pattern: "*{report.txt}" - - splitting_report: - type: file - description: Bismark splitting reports - pattern: "*{splitting_report.txt}" - - dedup_report: - type: file - description: Bismark deduplication reports - pattern: "*.{deduplication_report.txt}" - - mbias: - type: file - description: Text file containing methylation bias information - pattern: "*.{txt}" - - fasta: - type: file - description: Input genome fasta file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - align_report: + type: file + description: Bismark alignment reports + pattern: "*{report.txt}" + - dedup_report: + type: file + description: Bismark deduplication reports + pattern: "*.{deduplication_report.txt}" + - splitting_report: + type: file + description: Bismark splitting reports + pattern: "*{splitting_report.txt}" + - mbias: + type: file + description: Text file containing methylation bias information + pattern: "*.{txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - report: - type: file - description: Bismark reports - pattern: "*.{html,txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*report.{html,txt}": + type: file + description: Bismark reports + pattern: "*.{html,txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" +maintainers: + - "@phue" + - "@sateeshperi" diff --git a/modules/nf-core/bismark/report/nextflow.config b/modules/nf-core/bismark/report/nextflow.config new file mode 100644 index 00000000..597a4684 --- /dev/null +++ b/modules/nf-core/bismark/report/nextflow.config @@ -0,0 +1,10 @@ +process { + withName: BISMARK_REPORT { + ext.args = '' + publishDir = [ + path: "${params.outdir}/${params.aligner}/reports", + mode: params.publish_dir_mode, + pattern: "*.html" + ] + } +} \ No newline at end of file diff --git a/modules/nf-core/bismark/report/tests/main.nf.test b/modules/nf-core/bismark/report/tests/main.nf.test new file mode 100644 index 00000000..9082bbde --- /dev/null +++ b/modules/nf-core/bismark/report/tests/main.nf.test @@ -0,0 +1,88 @@ +nextflow_process { + + name "Test Process BISMARK_REPORT" + script "../main.nf" + process "BISMARK_REPORT" + + tag "modules" + tag "modules_nfcore" + tag "bismark" + tag "bismark/report" + tag "bismark/align" + tag "bismark/deduplicate" + tag "bismark/methylationextractor" + tag "bismark/genomepreparation" + + test("sarscov2 genome [fasta] | sarscov2 single-end methylated [fastq]") { + + setup { + run("BISMARK_GENOMEPREPARATION") { + script "../../genomepreparation/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + run("BISMARK_ALIGN") { + script "../../align/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ [ id:'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) + input[2] = BISMARK_GENOMEPREPARATION.out.index + """ + } + } + + run("BISMARK_DEDUPLICATE") { + script "../../deduplicate/main.nf" + process { + """ + input[0] = BISMARK_ALIGN.out.bam + """ + } + } + + run("BISMARK_METHYLATIONEXTRACTOR") { + script "../../methylationextractor/main.nf" + process { + """ + input[0] = BISMARK_ALIGN.out.bam + input[1] = BISMARK_GENOMEPREPARATION.out.index + """ + } + } + } + + when { + process { + """ + input[0] = BISMARK_ALIGN.out.report + .join(BISMARK_DEDUPLICATE.out.report) + .join(BISMARK_METHYLATIONEXTRACTOR.out.report) + .join(BISMARK_METHYLATIONEXTRACTOR.out.mbias) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.report[0][1]).name, + process.out.versions + ).match() }, + ) + } + + } + +} diff --git a/modules/nf-core/bismark/report/tests/main.nf.test.snap b/modules/nf-core/bismark/report/tests/main.nf.test.snap new file mode 100644 index 00000000..e1ebf022 --- /dev/null +++ b/modules/nf-core/bismark/report/tests/main.nf.test.snap @@ -0,0 +1,15 @@ +{ + "sarscov2 genome [fasta] | sarscov2 single-end methylated [fastq]": { + "content": [ + "test.methylated_1_bismark_bt2_SE_report.html", + [ + "versions.yml:md5,12d0b9440211d6540bbdc42e14fa18e6" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-14T18:47:46.955822618" + } +} diff --git a/modules/nf-core/bismark/summary/environment.yml b/modules/nf-core/bismark/summary/environment.yml new file mode 100644 index 00000000..9bc4753b --- /dev/null +++ b/modules/nf-core/bismark/summary/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::bismark=0.24.2 diff --git a/modules/nf-core/bismark/summary/main.nf b/modules/nf-core/bismark/summary/main.nf index 399f960d..2aadfc03 100644 --- a/modules/nf-core/bismark/summary/main.nf +++ b/modules/nf-core/bismark/summary/main.nf @@ -1,10 +1,10 @@ process BISMARK_SUMMARY { label 'process_low' - conda "bioconda::bismark=0.24.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bismark:0.24.0--hdfd78af_0' : - 'biocontainers/bismark:0.24.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/bismark:0.24.2--hdfd78af_0' : + 'biocontainers/bismark:0.24.2--hdfd78af_0' }" input: val(bam) @@ -14,8 +14,8 @@ process BISMARK_SUMMARY { path(mbias) output: - path "*report.{html,txt}", emit: summary - path "versions.yml" , emit: versions + path("*report.{html,txt}"), emit: summary + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -30,4 +30,17 @@ process BISMARK_SUMMARY { bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.report.txt + touch ${prefix}.report.html + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/bismark/summary/meta.yml b/modules/nf-core/bismark/summary/meta.yml index 96814826..da18a5c8 100644 --- a/modules/nf-core/bismark/summary/meta.yml +++ b/modules/nf-core/bismark/summary/meta.yml @@ -21,35 +21,41 @@ tools: documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 licence: ["GPL-3.0-or-later"] + identifier: biotools:bismark input: - - bam: - type: value - description: Array of Bismark alignment BAM filenames - pattern: "*.bam" - - align_report: - type: file - description: Bismark alignment reports - pattern: "*report.txt" - - dedup_report: - type: file - description: Bismark deduplication reports - pattern: "*.deduplication_report.txt" - - splitting_report: - type: file - description: Bismark splitting reports - pattern: "*splitting_report.txt" - - mbias: - type: file - description: Text file containing methylation bias information - pattern: "*.txt" + - - bam: + type: list + description: List of Bismark alignment BAM filenames + pattern: "*.bam" + - - align_report: + type: file + description: Bismark alignment reports + pattern: "*report.txt" + - - dedup_report: + type: file + description: Bismark deduplication reports + pattern: "*.deduplication_report.txt" + - - splitting_report: + type: file + description: Bismark splitting reports + pattern: "*splitting_report.txt" + - - mbias: + type: file + description: Text file containing methylation bias information + pattern: "*.txt" output: - summary: - type: file - description: Bismark summary - pattern: "*.{html,txt}" + - "*report.{html,txt}": + type: file + description: Bismark summary + pattern: "*.{html,txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" +maintainers: + - "@phue" + - "@sateeshperi" diff --git a/modules/nf-core/bismark/summary/nextflow.config b/modules/nf-core/bismark/summary/nextflow.config new file mode 100644 index 00000000..ded23dda --- /dev/null +++ b/modules/nf-core/bismark/summary/nextflow.config @@ -0,0 +1,10 @@ +process { + withName: BISMARK_SUMMARY { + ext.args = '' + publishDir = [ + path: "${params.outdir}/${params.aligner}/summary", + mode: params.publish_dir_mode, + pattern: "*.{html,txt}" + ] + } +} \ No newline at end of file diff --git a/modules/nf-core/bismark/summary/tests/main.nf.test b/modules/nf-core/bismark/summary/tests/main.nf.test new file mode 100644 index 00000000..046a5959 --- /dev/null +++ b/modules/nf-core/bismark/summary/tests/main.nf.test @@ -0,0 +1,94 @@ +nextflow_process { + + name "Test Process BISMARK_SUMMARY" + script "../main.nf" + process "BISMARK_SUMMARY" + + tag "modules" + tag "modules_nfcore" + tag "bismark" + tag "bismark/summary" + tag "bismark/align" + tag "bismark/deduplicate" + tag "bismark/genomepreparation" + tag "bismark/methylationextractor" + + test("sarscov2 genome [fasta] | sarscov2 single-end methylated [fastq]") { + + setup { + run("BISMARK_GENOMEPREPARATION") { + script "../../genomepreparation/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + run("BISMARK_ALIGN") { + script "../../align/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ [ id:'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) + input[2] = BISMARK_GENOMEPREPARATION.out.index + """ + } + } + + run("BISMARK_DEDUPLICATE") { + script "../../deduplicate/main.nf" + process { + """ + input[0] = BISMARK_ALIGN.out.bam + """ + } + } + + run("BISMARK_METHYLATIONEXTRACTOR") { + script "../../methylationextractor/main.nf" + process { + """ + input[0] = BISMARK_ALIGN.out.bam + input[1] = BISMARK_GENOMEPREPARATION.out.index + """ + } + } + } + + when { + process { + """ + input[0] = BISMARK_ALIGN.out.bam.collect { meta, bam -> bam } + input[1] = BISMARK_ALIGN.out.report.collect { meta, report -> report } + input[2] = BISMARK_DEDUPLICATE.out.report.collect { meta, report -> report } + input[3] = BISMARK_METHYLATIONEXTRACTOR.out.report.collect { meta, report -> report } + input[4] = BISMARK_METHYLATIONEXTRACTOR.out.mbias.collect { meta, txt -> txt } + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match("versions") }, + { + with(process.out.summary) { + assert get(0).size() == 2 + assert get(0).every { it.contains('bismark_summary_report') } + assert path(get(0).get(1)).readLines().first().contains('CpGs') + assert path(get(0).get(0)).readLines().last().contains('') + } + } + ) + } + + } + +} diff --git a/modules/nf-core/bismark/summary/tests/main.nf.test.snap b/modules/nf-core/bismark/summary/tests/main.nf.test.snap new file mode 100644 index 00000000..d9d0209e --- /dev/null +++ b/modules/nf-core/bismark/summary/tests/main.nf.test.snap @@ -0,0 +1,14 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,daa43bc3da654ba5a8acbc9d272a9e90" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-14T18:31:02.192850471" + } +} \ No newline at end of file diff --git a/modules/nf-core/bwameth/align/environment.yml b/modules/nf-core/bwameth/align/environment.yml new file mode 100644 index 00000000..707376eb --- /dev/null +++ b/modules/nf-core/bwameth/align/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::bwameth=0.2.7 diff --git a/modules/nf-core/bwameth/align/main.nf b/modules/nf-core/bwameth/align/main.nf index 47304035..2e6ff2d0 100644 --- a/modules/nf-core/bwameth/align/main.nf +++ b/modules/nf-core/bwameth/align/main.nf @@ -2,14 +2,15 @@ process BWAMETH_ALIGN { tag "$meta.id" label 'process_high' - conda "bioconda::bwameth=0.2.2" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bwameth:0.2.2--py_1' : - 'biocontainers/bwameth:0.2.2--py_1' }" + 'https://depot.galaxyproject.org/singularity/bwameth:0.2.7--pyh7cba7a3_0' : + 'biocontainers/bwameth:0.2.7--pyh7cba7a3_0' }" input: tuple val(meta), path(reads) - path index + tuple val(meta2), path(fasta) + tuple val(meta3), path(index) output: tuple val(meta), path("*.bam"), emit: bam @@ -24,23 +25,36 @@ process BWAMETH_ALIGN { def prefix = task.ext.prefix ?: "${meta.id}" def read_group = meta.read_group ? "-R ${meta.read_group}" : "" """ - INDEX=`find -L ${index} -name "*.bwameth.c2t" | sed 's/\\.bwameth.c2t\$//'` - # Modify the timestamps so that bwameth doesn't complain about building the index # See https://github.com/nf-core/methylseq/pull/217 - touch -c -- * + touch -c $index/* + + if [ ! -f $index/$fasta ]; then + ln -s \$(readlink $fasta) $index/$fasta; + fi bwameth.py \\ $args \\ $read_group \\ -t $task.cpus \\ - --reference \$INDEX \\ + --reference $index/$fasta \\ $reads \\ | samtools view $args2 -@ $task.cpus -bhS -o ${prefix}.bam - cat <<-END_VERSIONS > versions.yml "${task.process}": - bwameth: \$(echo \$(bwameth.py --version 2>&1) | cut -f2 -d" ") + bwameth: \$(bwameth.py --version | cut -f2 -d" ") + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bwameth: \$(bwameth.py --version | cut -f2 -d" ") END_VERSIONS """ } diff --git a/modules/nf-core/bwameth/align/meta.yml b/modules/nf-core/bwameth/align/meta.yml index 7d22bc84..593d1730 100644 --- a/modules/nf-core/bwameth/align/meta.yml +++ b/modules/nf-core/bwameth/align/meta.yml @@ -21,33 +21,51 @@ tools: documentation: https://github.com/brentp/bwa-meth arxiv: arXiv:1401.1129 licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - index: - type: dir - description: Directory containing bwameth genome index + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - index: + type: directory + description: Directory containing bwameth genome index output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" +maintainers: + - "@phue" diff --git a/modules/nf-core/bwameth/align/nextflow.config b/modules/nf-core/bwameth/align/nextflow.config new file mode 100644 index 00000000..d5cbe70d --- /dev/null +++ b/modules/nf-core/bwameth/align/nextflow.config @@ -0,0 +1,11 @@ +process { + withName: BWAMETH_ALIGN { + ext.args = '' + publishDir = [ + path: { "${params.outdir}/${params.aligner}/alignments" }, + pattern: "*.bam", + mode: params.publish_dir_mode, + enabled: params.save_align_intermeds + ] + } +} \ No newline at end of file diff --git a/modules/nf-core/bwameth/align/tests/main.nf.test b/modules/nf-core/bwameth/align/tests/main.nf.test new file mode 100644 index 00000000..37dd4ad2 --- /dev/null +++ b/modules/nf-core/bwameth/align/tests/main.nf.test @@ -0,0 +1,121 @@ + +nextflow_process { + + name "Test Process BWAMETH_ALIGN" + script "../main.nf" + process "BWAMETH_ALIGN" + + tag "modules" + tag "modules_nfcore" + tag "bwameth" + tag "bwameth/align" + tag "bwameth/index" + + setup { + run("BWAMETH_INDEX") { + script "../../../bwameth/index/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + } + + test("sarscov2 methylated single_end [fastq]") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = BWAMETH_INDEX.out.index + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.versions + ).match() + } + ) + } + } + + test("sarscov2 methylated paired_end [fastq]") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = BWAMETH_INDEX.out.index + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.versions + ).match() + } + ) + } + } + + test("sarscov2 methylated paired_end [fastq] - stub") { + options '-stub' + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = BWAMETH_INDEX.out.index + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/bwameth/align/tests/main.nf.test.snap b/modules/nf-core/bwameth/align/tests/main.nf.test.snap new file mode 100644 index 00000000..8f44bb78 --- /dev/null +++ b/modules/nf-core/bwameth/align/tests/main.nf.test.snap @@ -0,0 +1,63 @@ +{ + "sarscov2 methylated single_end [fastq]": { + "content": [ + "5fdda0ada69daa3956c65a24c9d1c1e0", + [ + "versions.yml:md5,c00660f78aeab4fabe00092c70656098" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-16T07:50:08.241201566" + }, + "sarscov2 methylated paired_end [fastq]": { + "content": [ + "cbd5cfa8b446e26987898a45a94770ba", + [ + "versions.yml:md5,c00660f78aeab4fabe00092c70656098" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-16T07:50:20.75109829" + }, + "sarscov2 methylated paired_end [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,c00660f78aeab4fabe00092c70656098" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,c00660f78aeab4fabe00092c70656098" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-21T12:43:43.563953696" + } +} \ No newline at end of file diff --git a/modules/nf-core/bwameth/index/environment.yml b/modules/nf-core/bwameth/index/environment.yml new file mode 100644 index 00000000..707376eb --- /dev/null +++ b/modules/nf-core/bwameth/index/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::bwameth=0.2.7 diff --git a/modules/nf-core/bwameth/index/main.nf b/modules/nf-core/bwameth/index/main.nf index 1c789885..b4327a7b 100644 --- a/modules/nf-core/bwameth/index/main.nf +++ b/modules/nf-core/bwameth/index/main.nf @@ -2,17 +2,17 @@ process BWAMETH_INDEX { tag "$fasta" label 'process_high' - conda "bioconda::bwameth=0.2.2" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bwameth:0.2.2--py_1' : - 'biocontainers/bwameth:0.2.2--py_1' }" + 'https://depot.galaxyproject.org/singularity/bwameth:0.2.7--pyh7cba7a3_0' : + 'biocontainers/bwameth:0.2.7--pyh7cba7a3_0' }" input: - path fasta, stageAs: "bwameth/*" + tuple val(meta), path(fasta, name:"BwamethIndex/") output: - path "bwameth" , emit: index - path "versions.yml" , emit: versions + tuple val(meta), path("BwamethIndex"), emit: index + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -20,11 +20,34 @@ process BWAMETH_INDEX { script: def args = task.ext.args ?: '' """ + bwameth.py index $fasta + rm $fasta + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bwameth: \$(bwameth.py --version | cut -f2 -d" ") + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + """ + rm $fasta + + mkdir -p BwamethIndex/ + touch BwamethIndex/genome.fasta.bwameth.c2t + touch BwamethIndex/genome.fasta.bwameth.c2t.amb + touch BwamethIndex/genome.fasta.bwameth.c2t.ann + touch BwamethIndex/genome.fasta.bwameth.c2t.bwt + touch BwamethIndex/genome.fasta.bwameth.c2t.pac + touch BwamethIndex/genome.fasta.bwameth.c2t.sa + + cat <<-END_VERSIONS > versions.yml "${task.process}": - bwameth: \$(echo \$(bwameth.py --version 2>&1) | cut -f2 -d" ") + bwameth: \$(bwameth.py --version | cut -f2 -d" ") END_VERSIONS """ } diff --git a/modules/nf-core/bwameth/index/meta.yml b/modules/nf-core/bwameth/index/meta.yml index 903ae95c..2194e225 100644 --- a/modules/nf-core/bwameth/index/meta.yml +++ b/modules/nf-core/bwameth/index/meta.yml @@ -17,18 +17,33 @@ tools: documentation: https://github.com/brentp/bwa-meth arxiv: arXiv:1401.1129 licence: ["MIT"] + identifier: "" input: - - fasta: - type: file - description: Input genome fasta file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file output: - index: - type: dir - description: Directory containing bwameth genome index - pattern: "index" + - meta: + type: directory + description: Directory containing bwameth genome index + pattern: "index" + - BwamethIndex: + type: directory + description: Directory containing bwameth genome index + pattern: "index" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" +maintainers: + - "@phue" + - "@sateeshperi" diff --git a/modules/nf-core/bwameth/index/nextflow.config b/modules/nf-core/bwameth/index/nextflow.config new file mode 100644 index 00000000..92d4e632 --- /dev/null +++ b/modules/nf-core/bwameth/index/nextflow.config @@ -0,0 +1,11 @@ +process { + withName: BWAMETH_INDEX { + ext.args = '' + publishDir = [ + path: { "${params.outdir}/${params.aligner}/reference_genome" }, + mode: params.publish_dir_mode, + saveAs: { it.equals('versions.yml') ? null : it.tokenize("/").last() }, + enabled: params.save_reference + ] + } +} \ No newline at end of file diff --git a/modules/nf-core/bwameth/index/tests/main.nf.test b/modules/nf-core/bwameth/index/tests/main.nf.test new file mode 100644 index 00000000..152c8366 --- /dev/null +++ b/modules/nf-core/bwameth/index/tests/main.nf.test @@ -0,0 +1,34 @@ + +nextflow_process { + + name "Test Process BWAMETH_INDEX" + script "../main.nf" + process "BWAMETH_INDEX" + + tag "modules" + tag "modules_nfcore" + tag "bwameth" + tag "bwameth/index" + + test("sarscov2 genome [fasta]") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/bwameth/index/tests/main.nf.test.snap b/modules/nf-core/bwameth/index/tests/main.nf.test.snap new file mode 100644 index 00000000..fb427880 --- /dev/null +++ b/modules/nf-core/bwameth/index/tests/main.nf.test.snap @@ -0,0 +1,49 @@ +{ + "sarscov2 genome [fasta]": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "genome.fasta.bwameth.c2t:md5,98039984526a41d04d6bd92fcc040c62", + "genome.fasta.bwameth.c2t.amb:md5,249a4195069071ce47cd0bae68abe376", + "genome.fasta.bwameth.c2t.ann:md5,46524d4359dcdfb203a235ab3b930dbb", + "genome.fasta.bwameth.c2t.bwt:md5,84f65df7d42dbe84c9ccfaddfdd5ea6b", + "genome.fasta.bwameth.c2t.pac:md5,4d8e51cb0bbdeaf24576bdf0264d8653", + "genome.fasta.bwameth.c2t.sa:md5,d25f6486f5134f57ed5b258f6fbb8673" + ] + ] + ], + "1": [ + "versions.yml:md5,0827d461c1a0b41bd533aea470843c2c" + ], + "index": [ + [ + { + "id": "test" + }, + [ + "genome.fasta.bwameth.c2t:md5,98039984526a41d04d6bd92fcc040c62", + "genome.fasta.bwameth.c2t.amb:md5,249a4195069071ce47cd0bae68abe376", + "genome.fasta.bwameth.c2t.ann:md5,46524d4359dcdfb203a235ab3b930dbb", + "genome.fasta.bwameth.c2t.bwt:md5,84f65df7d42dbe84c9ccfaddfdd5ea6b", + "genome.fasta.bwameth.c2t.pac:md5,4d8e51cb0bbdeaf24576bdf0264d8653", + "genome.fasta.bwameth.c2t.sa:md5,d25f6486f5134f57ed5b258f6fbb8673" + ] + ] + ], + "versions": [ + "versions.yml:md5,0827d461c1a0b41bd533aea470843c2c" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-14T20:32:13.750317299" + } +} \ No newline at end of file diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml new file mode 100644 index 00000000..71e04c3d --- /dev/null +++ b/modules/nf-core/cat/fastq/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - conda-forge::coreutils=9.5 diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index 5021e6fc..4364a389 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -2,10 +2,10 @@ process CAT_FASTQ { tag "$meta.id" label 'process_single' - conda "conda-forge::sed=4.7" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'nf-core/ubuntu:20.04' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data' : + 'community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264' }" input: tuple val(meta), path(reads, stageAs: "input*/*") @@ -53,9 +53,9 @@ process CAT_FASTQ { def prefix = task.ext.prefix ?: "${meta.id}" def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()] if (meta.single_end) { - if (readList.size > 1) { + if (readList.size >= 1) { """ - touch ${prefix}.merged.fastq.gz + echo '' | gzip > ${prefix}.merged.fastq.gz cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -64,10 +64,10 @@ process CAT_FASTQ { """ } } else { - if (readList.size > 2) { + if (readList.size >= 2) { """ - touch ${prefix}_1.merged.fastq.gz - touch ${prefix}_2.merged.fastq.gz + echo '' | gzip > ${prefix}_1.merged.fastq.gz + echo '' | gzip > ${prefix}_2.merged.fastq.gz cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -76,5 +76,4 @@ process CAT_FASTQ { """ } } - } diff --git a/modules/nf-core/cat/fastq/meta.yml b/modules/nf-core/cat/fastq/meta.yml index 8a39e309..91ff2fb5 100644 --- a/modules/nf-core/cat/fastq/meta.yml +++ b/modules/nf-core/cat/fastq/meta.yml @@ -10,31 +10,36 @@ tools: The cat utility reads files sequentially, writing them to the standard output. documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files to be concatenated. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files to be concatenated. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: Merged fastq file - pattern: "*.{merged.fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.merged.fastq.gz": + type: file + description: Merged fastq file + pattern: "*.{merged.fastq.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" +maintainers: + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test b/modules/nf-core/cat/fastq/tests/main.nf.test new file mode 100644 index 00000000..f88a78b6 --- /dev/null +++ b/modules/nf-core/cat/fastq/tests/main.nf.test @@ -0,0 +1,248 @@ +// NOTE The version snaps may not be consistant +// https://github.com/nf-core/modules/pull/4087#issuecomment-1767948035 +nextflow_process { + + name "Test Process CAT_FASTQ" + script "../main.nf" + process "CAT_FASTQ" + tag "modules" + tag "modules_nfcore" + tag "cat" + tag "cat/fastq" + + test("test_cat_fastq_single_end") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_paired_end") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_single_end_same_name") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_paired_end_same_name") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_single_end_single_file") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_single_end - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_paired_end - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_single_end_same_name - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_paired_end_same_name - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_single_end_single_file - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test.snap b/modules/nf-core/cat/fastq/tests/main.nf.test.snap new file mode 100644 index 00000000..f8689a1c --- /dev/null +++ b/modules/nf-core/cat/fastq/tests/main.nf.test.snap @@ -0,0 +1,376 @@ +{ + "test_cat_fastq_single_end": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,ee314a9bd568d06617171b0c85f508da" + ] + ], + "1": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,ee314a9bd568d06617171b0c85f508da" + ] + ], + "versions": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-19T20:02:07.519211144" + }, + "test_cat_fastq_single_end_same_name": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22" + ] + ], + "1": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22" + ] + ], + "versions": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-19T20:02:31.618628921" + }, + "test_cat_fastq_single_end_single_file": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-19T20:02:57.904149581" + }, + "test_cat_fastq_paired_end_same_name": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "1": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "versions": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-19T20:02:44.577183829" + }, + "test_cat_fastq_single_end - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-19T20:03:10.603734777" + }, + "test_cat_fastq_paired_end_same_name - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "1": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "versions": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-19T20:03:46.041808828" + }, + "test_cat_fastq_single_end_same_name - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-19T20:03:34.13865402" + }, + "test_cat_fastq_paired_end": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "1": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "versions": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-19T20:02:19.64383573" + }, + "test_cat_fastq_paired_end - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "1": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "versions": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-19T20:03:22.597246066" + }, + "test_cat_fastq_single_end_single_file - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-19T20:03:58.44849001" + } +} \ No newline at end of file diff --git a/modules/nf-core/cat/fastq/tests/tags.yml b/modules/nf-core/cat/fastq/tests/tags.yml new file mode 100644 index 00000000..6ac43614 --- /dev/null +++ b/modules/nf-core/cat/fastq/tests/tags.yml @@ -0,0 +1,2 @@ +cat/fastq: + - modules/nf-core/cat/fastq/** diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml deleted file mode 100644 index f0c63f69..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: custom_dumpsoftwareversions -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - bioconda::multiqc=1.17 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf deleted file mode 100644 index 7685b33c..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ /dev/null @@ -1,24 +0,0 @@ -process CUSTOM_DUMPSOFTWAREVERSIONS { - label 'process_single' - - // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.17--pyhdfd78af_0' : - 'biocontainers/multiqc:1.17--pyhdfd78af_0' }" - - input: - path versions - - output: - path "software_versions.yml" , emit: yml - path "software_versions_mqc.yml", emit: mqc_yml - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - template 'dumpsoftwareversions.py' -} diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml deleted file mode 100644 index 5f15a5fd..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ /dev/null @@ -1,37 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json -name: custom_dumpsoftwareversions -description: Custom module used to dump software versions within the nf-core pipeline template -keywords: - - custom - - dump - - version -tools: - - custom: - description: Custom module used to dump software versions within the nf-core pipeline template - homepage: https://github.com/nf-core/tools - documentation: https://github.com/nf-core/tools - licence: ["MIT"] -input: - - versions: - type: file - description: YML file containing software versions - pattern: "*.yml" -output: - - yml: - type: file - description: Standard YML file containing software versions - pattern: "software_versions.yml" - - mqc_yml: - type: file - description: MultiQC custom content YML file containing software versions - pattern: "software_versions_mqc.yml" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@drpatelh" - - "@grst" -maintainers: - - "@drpatelh" - - "@grst" diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py deleted file mode 100755 index da033408..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ /dev/null @@ -1,101 +0,0 @@ -#!/usr/bin/env python - - -"""Provide functions to merge multiple versions.yml files.""" - - -import yaml -import platform -from textwrap import dedent - - -def _make_versions_html(versions): - """Generate a tabular HTML output of all versions for MultiQC.""" - html = [ - dedent( - """\\ - - - - - - - - - - """ - ) - ] - for process, tmp_versions in sorted(versions.items()): - html.append("") - for i, (tool, version) in enumerate(sorted(tmp_versions.items())): - html.append( - dedent( - f"""\\ - - - - - - """ - ) - ) - html.append("") - html.append("
    Process Name Software Version
    {process if (i == 0) else ''}{tool}{version}
    ") - return "\\n".join(html) - - -def main(): - """Load all version files and generate merged output.""" - versions_this_module = {} - versions_this_module["${task.process}"] = { - "python": platform.python_version(), - "yaml": yaml.__version__, - } - - with open("$versions") as f: - versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module - - # aggregate versions by the module name (derived from fully-qualified process name) - versions_by_module = {} - for process, process_versions in versions_by_process.items(): - module = process.split(":")[-1] - try: - if versions_by_module[module] != process_versions: - raise AssertionError( - "We assume that software versions are the same between all modules. " - "If you see this error-message it means you discovered an edge-case " - "and should open an issue in nf-core/tools. " - ) - except KeyError: - versions_by_module[module] = process_versions - - versions_by_module["Workflow"] = { - "Nextflow": "$workflow.nextflow.version", - "$workflow.manifest.name": "$workflow.manifest.version", - } - - versions_mqc = { - "id": "software_versions", - "section_name": "${workflow.manifest.name} Software Versions", - "section_href": "https://github.com/${workflow.manifest.name}", - "plot_type": "html", - "description": "are collected at run time from the software output.", - "data": _make_versions_html(versions_by_module), - } - - with open("software_versions.yml", "w") as f: - yaml.dump(versions_by_module, f, default_flow_style=False) - with open("software_versions_mqc.yml", "w") as f: - yaml.dump(versions_mqc, f, default_flow_style=False) - - with open("versions.yml", "w") as f: - yaml.dump(versions_this_module, f, default_flow_style=False) - - -if __name__ == "__main__": - main() diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test deleted file mode 100644 index b1e1630b..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test +++ /dev/null @@ -1,43 +0,0 @@ -nextflow_process { - - name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS" - script "../main.nf" - process "CUSTOM_DUMPSOFTWAREVERSIONS" - tag "modules" - tag "modules_nfcore" - tag "custom" - tag "dumpsoftwareversions" - tag "custom/dumpsoftwareversions" - - test("Should run without failures") { - when { - process { - """ - def tool1_version = ''' - TOOL1: - tool1: 0.11.9 - '''.stripIndent() - - def tool2_version = ''' - TOOL2: - tool2: 1.9 - '''.stripIndent() - - input[0] = Channel.of(tool1_version, tool2_version).collectFile() - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.versions, - file(process.out.mqc_yml[0]).readLines()[0..10], - file(process.out.yml[0]).readLines()[0..7] - ).match() - } - ) - } - } -} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap deleted file mode 100644 index 29e72446..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap +++ /dev/null @@ -1,33 +0,0 @@ -{ - "Should run without failures": { - "content": [ - [ - "versions.yml:md5,3843ac526e762117eedf8825b40683df" - ], - [ - "data: \"\\n\\n \\n \\n \\n \\n \\n \\n \\n\\", - " \\n\\n\\n \\n \\n\\", - " \\ \\n\\n\\n\\n \\n \\", - " \\ \\n \\n\\n\\n\\n\\", - " \\n\\n \\n \\n\\", - " \\ \\n\\n\\n\\n\\n\\n \\n\\", - " \\ \\n \\n\\n\\n\\n\\", - " \\n\\n \\n \\n\\" - ], - [ - "CUSTOM_DUMPSOFTWAREVERSIONS:", - " python: 3.12.0", - " yaml: 6.0.1", - "TOOL1:", - " tool1: 0.11.9", - "TOOL2:", - " tool2: '1.9'", - "Workflow:" - ] - ], - "timestamp": "2024-01-05T00:18:43.461970077" - } -} \ No newline at end of file diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml deleted file mode 100644 index 405aa24a..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -custom/dumpsoftwareversions: - - modules/nf-core/custom/dumpsoftwareversions/** diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index 1787b38a..691d4c76 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -1,7 +1,5 @@ -name: fastqc channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 9e19a74c..d8989f48 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -25,6 +25,14 @@ process FASTQC { def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] } def rename_to = old_new_pairs*.join(' ').join(' ') def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') + + // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory) + // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222 + // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label + def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus + // FastQC memory value allowed range (100 - 10000) + def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) + """ printf "%s %s\\n" $rename_to | while read old_name new_name; do [ -f "\${new_name}" ] || ln -s \$old_name \$new_name @@ -33,6 +41,7 @@ process FASTQC { fastqc \\ $args \\ --threads $task.cpus \\ + --memory $fastqc_memory \\ $renamed_files cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index ee5507e0..4827da7a 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -16,35 +16,44 @@ tools: homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ licence: ["GPL-2.0-only"] + identifier: biotools:fastqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - html: - type: file - description: FastQC report - pattern: "*_{fastqc.html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: FastQC report + pattern: "*_{fastqc.html}" - zip: - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.zip": + type: file + description: FastQC report archive + pattern: "*_{fastqc.zip}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/fastqc/nextflow.config b/modules/nf-core/fastqc/nextflow.config new file mode 100644 index 00000000..7e31c74d --- /dev/null +++ b/modules/nf-core/fastqc/nextflow.config @@ -0,0 +1,17 @@ +process { + withName: FASTQC { + ext.args = '--quiet' + publishDir = [ + [ + path: { "${params.outdir}/fastqc" }, + mode: params.publish_dir_mode, + pattern: "*.html" + ], + [ + path: { "${params.outdir}/fastqc/zips" }, + mode: params.publish_dir_mode, + pattern: "*.zip" + ] + ] + } +} \ No newline at end of file diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index b9e8f926..e9d79a07 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -3,107 +3,307 @@ nextflow_process { name "Test Process FASTQC" script "../main.nf" process "FASTQC" + tag "modules" tag "modules_nfcore" tag "fastqc" - test("Single-Read") { + test("sarscov2 single-end [fastq]") { when { - params { - outdir = "$outputDir" + process { + """ + input[0] = Channel.of([ + [ id: 'test', single_end:true ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] + ]) + """ } + } + + then { + assertAll ( + { assert process.success }, + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. + // looks like this:
    Mon 2 Oct 2023
    test.gz
    + // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + { assert snapshot(process.out.versions).match() } + ) + } + } + + test("sarscov2 paired-end [fastq]") { + + when { process { """ - input[0] = [ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("") }, + { assert path(process.out.html[0][1][1]).text.contains("") }, + { assert snapshot(process.out.versions).match() } + ) + } + } + + test("sarscov2 interleaved [fastq]") { + + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + { assert snapshot(process.out.versions).match() } + ) + } + } + + test("sarscov2 paired-end [bam]") { + + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + { assert snapshot(process.out.versions).match() } + ) + } + } + + test("sarscov2 multiple [fastq]") { + + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, + { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, + { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("") }, + { assert path(process.out.html[0][1][1]).text.contains("") }, + { assert path(process.out.html[0][1][2]).text.contains("") }, + { assert path(process.out.html[0][1][3]).text.contains("") }, + { assert snapshot(process.out.versions).match() } + ) + } + } + + test("sarscov2 custom_prefix") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'mysample', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + { assert snapshot(process.out.versions).match() } + ) + } + } + + test("sarscov2 single-end [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ [ id: 'test', single_end:true ], - [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) - ] - ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 paired-end [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 interleaved [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 paired-end [bam] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 multiple [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 custom_prefix - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'mysample', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ]) """ } } then { assertAll ( - { assert process.success }, - // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. - // looks like this:
    Mon 2 Oct 2023
    test.gz
    - // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 - { assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html" }, - { assert path(process.out.html.get(0).get(1)).getText().contains("") }, - { assert snapshot(process.out.versions).match("versions") }, - { assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip" } + { assert process.success }, + { assert snapshot(process.out).match() } ) } } -// TODO -// // -// // Test with paired-end data -// // -// workflow test_fastqc_paired_end { -// input = [ -// [id: 'test', single_end: false], // meta map -// [ -// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), -// file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) -// ] -// ] - -// FASTQC ( input ) -// } - -// // -// // Test with interleaved data -// // -// workflow test_fastqc_interleaved { -// input = [ -// [id: 'test', single_end: false], // meta map -// file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true) -// ] - -// FASTQC ( input ) -// } - -// // -// // Test with bam data -// // -// workflow test_fastqc_bam { -// input = [ -// [id: 'test', single_end: false], // meta map -// file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) -// ] - -// FASTQC ( input ) -// } - -// // -// // Test with multiple samples -// // -// workflow test_fastqc_multiple { -// input = [ -// [id: 'test', single_end: false], // meta map -// [ -// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), -// file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true), -// file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true), -// file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true) -// ] -// ] - -// FASTQC ( input ) -// } - -// // -// // Test with custom prefix -// // -// workflow test_fastqc_custom_prefix { -// input = [ -// [ id:'mysample', single_end:true ], // meta map -// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) -// ] - -// FASTQC ( input ) -// } } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap index 636a32ce..d5db3092 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,10 +1,392 @@ { - "versions": { + "sarscov2 custom_prefix": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], - "timestamp": "2023-10-09T23:40:54+0000" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:16.374038" + }, + "sarscov2 single-end [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": true + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": true + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:24.993809" + }, + "sarscov2 custom_prefix - stub": { + "content": [ + { + "0": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:03:10.93942" + }, + "sarscov2 interleaved [fastq]": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:01:42.355718" + }, + "sarscov2 paired-end [bam]": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:01:53.276274" + }, + "sarscov2 multiple [fastq]": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:05.527626" + }, + "sarscov2 paired-end [fastq]": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:01:31.188871" + }, + "sarscov2 paired-end [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:34.273566" + }, + "sarscov2 multiple [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:03:02.304411" + }, + "sarscov2 single-end [fastq]": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:01:19.095607" + }, + "sarscov2 interleaved [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:44.640184" + }, + "sarscov2 paired-end [bam] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:53.550742" } } \ No newline at end of file diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml new file mode 100644 index 00000000..c7794856 --- /dev/null +++ b/modules/nf-core/gunzip/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda +dependencies: + - conda-forge::grep=3.11 + - conda-forge::sed=4.8 + - conda-forge::tar=1.34 diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf new file mode 100644 index 00000000..5e67e3b9 --- /dev/null +++ b/modules/nf-core/gunzip/main.nf @@ -0,0 +1,55 @@ +process GUNZIP { + tag "$archive" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/ubuntu:22.04' : + 'nf-core/ubuntu:22.04' }" + + input: + tuple val(meta), path(archive) + + output: + tuple val(meta), path("$gunzip"), emit: gunzip + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def extension = ( archive.toString() - '.gz' ).tokenize('.')[-1] + def name = archive.toString() - '.gz' - ".$extension" + def prefix = task.ext.prefix ?: name + gunzip = prefix + ".$extension" + """ + # Not calling gunzip itself because it creates files + # with the original group ownership rather than the + # default one for that user / the work directory + gzip \\ + -cd \\ + $args \\ + $archive \\ + > $gunzip + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def extension = ( archive.toString() - '.gz' ).tokenize('.')[-1] + def name = archive.toString() - '.gz' - ".$extension" + def prefix = task.ext.prefix ?: name + gunzip = prefix + ".$extension" + """ + touch $gunzip + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml new file mode 100644 index 00000000..9066c035 --- /dev/null +++ b/modules/nf-core/gunzip/meta.yml @@ -0,0 +1,47 @@ +name: gunzip +description: Compresses and decompresses files. +keywords: + - gunzip + - compression + - decompression +tools: + - gunzip: + description: | + gzip is a file format and a software application used for file compression and decompression. + documentation: https://www.gnu.org/software/gzip/manual/gzip.html + licence: ["GPL-3.0-or-later"] + identifier: "" +input: + - - meta: + type: map + description: | + Optional groovy Map containing meta information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be compressed/uncompressed + pattern: "*.*" +output: + - gunzip: + - meta: + type: file + description: Compressed/uncompressed file + pattern: "*.*" + - $gunzip: + type: file + description: Compressed/uncompressed file + pattern: "*.*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@joseespinosa" + - "@drpatelh" + - "@jfy133" +maintainers: + - "@joseespinosa" + - "@drpatelh" + - "@jfy133" + - "@gallvp" diff --git a/modules/nf-core/gunzip/tests/main.nf.test b/modules/nf-core/gunzip/tests/main.nf.test new file mode 100644 index 00000000..776211ad --- /dev/null +++ b/modules/nf-core/gunzip/tests/main.nf.test @@ -0,0 +1,121 @@ +nextflow_process { + + name "Test Process GUNZIP" + script "../main.nf" + process "GUNZIP" + tag "gunzip" + tag "modules_nfcore" + tag "modules" + + test("Should run without failures") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("Should run without failures - prefix") { + + config './nextflow.config' + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("Should run without failures - stub") { + + options '-stub' + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("Should run without failures - prefix - stub") { + + options '-stub' + config './nextflow.config' + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gunzip/tests/main.nf.test.snap b/modules/nf-core/gunzip/tests/main.nf.test.snap new file mode 100644 index 00000000..069967e7 --- /dev/null +++ b/modules/nf-core/gunzip/tests/main.nf.test.snap @@ -0,0 +1,134 @@ +{ + "Should run without failures - prefix - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-25T11:35:10.861293" + }, + "Should run without failures - stub": { + "content": [ + { + "0": [ + [ + [ + + ], + "test_1.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + [ + + ], + "test_1.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-25T11:35:05.857145" + }, + "Should run without failures": { + "content": [ + { + "0": [ + [ + [ + + ], + "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + [ + + ], + "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2023-10-17T15:35:37.690477896" + }, + "Should run without failures - prefix": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-25T11:33:32.921739" + } +} \ No newline at end of file diff --git a/modules/nf-core/gunzip/tests/nextflow.config b/modules/nf-core/gunzip/tests/nextflow.config new file mode 100644 index 00000000..dec77642 --- /dev/null +++ b/modules/nf-core/gunzip/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: GUNZIP { + ext.prefix = { "${meta.id}.xyz" } + } +} diff --git a/modules/nf-core/gunzip/tests/tags.yml b/modules/nf-core/gunzip/tests/tags.yml new file mode 100644 index 00000000..fd3f6915 --- /dev/null +++ b/modules/nf-core/gunzip/tests/tags.yml @@ -0,0 +1,2 @@ +gunzip: + - modules/nf-core/gunzip/** diff --git a/modules/nf-core/methyldackel/extract/environment.yml b/modules/nf-core/methyldackel/extract/environment.yml new file mode 100644 index 00000000..34beddbe --- /dev/null +++ b/modules/nf-core/methyldackel/extract/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::methyldackel=0.6.1 diff --git a/modules/nf-core/methyldackel/extract/main.nf b/modules/nf-core/methyldackel/extract/main.nf index 32951459..66b2745a 100644 --- a/modules/nf-core/methyldackel/extract/main.nf +++ b/modules/nf-core/methyldackel/extract/main.nf @@ -2,10 +2,10 @@ process METHYLDACKEL_EXTRACT { tag "$meta.id" label 'process_medium' - conda "bioconda::methyldackel=0.6.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/methyldackel:0.6.0--h22771d5_0' : - 'biocontainers/methyldackel:0.6.0--h22771d5_0' }" + 'https://depot.galaxyproject.org/singularity/methyldackel:0.6.1--he4a0461_7' : + 'biocontainers/methyldackel:0.6.1--he4a0461_7' }" input: tuple val(meta), path(bam), path(bai) @@ -33,4 +33,16 @@ process METHYLDACKEL_EXTRACT { methyldackel: \$(MethylDackel --version 2>&1 | cut -f1 -d" ") END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + def out_extension = args.contains('--methylKit') ? 'methylKit' : 'bedGraph' + """ + touch ${bam.baseName}_CpG.${out_extension} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + methyldackel: \$(MethylDackel --version 2>&1 | cut -f1 -d" ") + END_VERSIONS + """ } diff --git a/modules/nf-core/methyldackel/extract/meta.yml b/modules/nf-core/methyldackel/extract/meta.yml index 9d777bb1..2f17738f 100644 --- a/modules/nf-core/methyldackel/extract/meta.yml +++ b/modules/nf-core/methyldackel/extract/meta.yml @@ -18,45 +18,56 @@ tools: homepage: https://github.com/dpryan79/MethylDackel documentation: https://github.com/dpryan79/MethylDackel/blob/master/README.md licence: ["MIT"] + identifier: biotools:methyldackel input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file - pattern: "*.{fasta,fa}" - - fai: - type: file - description: FASTA index file - pattern: "*.fai" - - bam: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - bai: - type: file - description: BAM/CRAM index file - pattern: "*.{bai,crai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - bai: + type: file + description: BAM/CRAM index file + pattern: "*.{bai,crai}" + - - fasta: + type: file + description: Input genome fasta file + pattern: "*.{fasta,fa}" + - - fai: + type: file + description: FASTA index file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bedgraph: - type: file - description: bedGraph file, containing per-base methylation metrics - pattern: "*.bedGraph" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bedGraph": + type: file + description: bedGraph file, containing per-base methylation metrics + pattern: "*.bedGraph" - methylkit: - type: file - description: methylKit file, containing per-base methylation metrics - pattern: "*.methylKit" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.methylKit": + type: file + description: methylKit file, containing per-base methylation metrics + pattern: "*.methylKit" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" +maintainers: + - "@phue" diff --git a/modules/nf-core/methyldackel/extract/nextflow.config b/modules/nf-core/methyldackel/extract/nextflow.config new file mode 100644 index 00000000..f7e24c73 --- /dev/null +++ b/modules/nf-core/methyldackel/extract/nextflow.config @@ -0,0 +1,22 @@ +process { + withName: METHYLDACKEL_EXTRACT { + ext.args = [ + params.comprehensive ? ' --CHG --CHH' : '', + params.ignore_flags ? " --ignoreFlags" : '', + params.methyl_kit ? " --methylKit" : '', + params.min_depth > 0 ? " --minDepth ${params.min_depth}" : '' + ].join(" ").trim() + publishDir = [ + [ + path: { "${params.outdir}/methyldackel" }, + mode: params.publish_dir_mode, + pattern: "*.bedGraph" + ], + [ + path: { "${params.outdir}/methyldackel" }, + mode: params.publish_dir_mode, + pattern: "*.methylKit" + ] + ] + } +} \ No newline at end of file diff --git a/modules/nf-core/methyldackel/extract/tests/main.nf.test b/modules/nf-core/methyldackel/extract/tests/main.nf.test new file mode 100644 index 00000000..562f5c2e --- /dev/null +++ b/modules/nf-core/methyldackel/extract/tests/main.nf.test @@ -0,0 +1,90 @@ + +nextflow_process { + + name "Test Process METHYLDACKEL_EXTRACT" + script "../main.nf" + process "METHYLDACKEL_EXTRACT" + + tag "modules" + tag "modules_nfcore" + tag "methyldackel" + tag "methyldackel/extract" + + test("test-methyldackel-extract") { + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-methyldackel-extract-methyl-kit") { + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-methyldackel-extract-methyl-kit-stub") { + config "./nextflow.config" + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/methyldackel/extract/tests/main.nf.test.snap b/modules/nf-core/methyldackel/extract/tests/main.nf.test.snap new file mode 100644 index 00000000..64cbd76b --- /dev/null +++ b/modules/nf-core/methyldackel/extract/tests/main.nf.test.snap @@ -0,0 +1,125 @@ +{ + "test-methyldackel-extract-methyl-kit": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.methylated.sorted_CpG.methylKit:md5,b1dc217909cd5f8174058c7af785f51c" + ] + ], + "2": [ + "versions.yml:md5,9e23b0c31bf0f98e9348321fe9226498" + ], + "bedgraph": [ + + ], + "methylkit": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.methylated.sorted_CpG.methylKit:md5,b1dc217909cd5f8174058c7af785f51c" + ] + ], + "versions": [ + "versions.yml:md5,9e23b0c31bf0f98e9348321fe9226498" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T20:34:17.513866" + }, + "test-methyldackel-extract-methyl-kit-stub": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.methylated.sorted_CpG.methylKit:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,9e23b0c31bf0f98e9348321fe9226498" + ], + "bedgraph": [ + + ], + "methylkit": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.methylated.sorted_CpG.methylKit:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,9e23b0c31bf0f98e9348321fe9226498" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T20:34:22.343382" + }, + "test-methyldackel-extract": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.methylated.sorted_CpG.bedGraph:md5,abcc9d1db6e48d5aced567c337b563d4" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,9e23b0c31bf0f98e9348321fe9226498" + ], + "bedgraph": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.methylated.sorted_CpG.bedGraph:md5,abcc9d1db6e48d5aced567c337b563d4" + ] + ], + "methylkit": [ + + ], + "versions": [ + "versions.yml:md5,9e23b0c31bf0f98e9348321fe9226498" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T20:34:12.605013" + } +} \ No newline at end of file diff --git a/modules/nf-core/methyldackel/extract/tests/nextflow.config b/modules/nf-core/methyldackel/extract/tests/nextflow.config new file mode 100644 index 00000000..4f7caeb4 --- /dev/null +++ b/modules/nf-core/methyldackel/extract/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: METHYLDACKEL_EXTRACT { + ext.args = "--methylKit" + } +} diff --git a/modules/nf-core/methyldackel/mbias/environment.yml b/modules/nf-core/methyldackel/mbias/environment.yml new file mode 100644 index 00000000..34beddbe --- /dev/null +++ b/modules/nf-core/methyldackel/mbias/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::methyldackel=0.6.1 diff --git a/modules/nf-core/methyldackel/mbias/main.nf b/modules/nf-core/methyldackel/mbias/main.nf index b30d3391..f0c48a34 100644 --- a/modules/nf-core/methyldackel/mbias/main.nf +++ b/modules/nf-core/methyldackel/mbias/main.nf @@ -2,10 +2,10 @@ process METHYLDACKEL_MBIAS { tag "$meta.id" label 'process_low' - conda "bioconda::methyldackel=0.6.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/methyldackel:0.6.0--h22771d5_0' : - 'biocontainers/methyldackel:0.6.0--h22771d5_0' }" + 'https://depot.galaxyproject.org/singularity/methyldackel:0.6.1--he4a0461_7' : + 'biocontainers/methyldackel:0.6.1--he4a0461_7' }" input: tuple val(meta), path(bam), path(bai) @@ -36,4 +36,15 @@ process METHYLDACKEL_MBIAS { methyldackel: \$(MethylDackel --version 2>&1 | cut -f1 -d" ") END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.mbias.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + methyldackel: \$(MethylDackel --version 2>&1 | cut -f1 -d" ") + END_VERSIONS + """ } diff --git a/modules/nf-core/methyldackel/mbias/meta.yml b/modules/nf-core/methyldackel/mbias/meta.yml index 75217232..10b3dcad 100644 --- a/modules/nf-core/methyldackel/mbias/meta.yml +++ b/modules/nf-core/methyldackel/mbias/meta.yml @@ -19,41 +19,46 @@ tools: homepage: https://github.com/dpryan79/MethylDackel documentation: https://github.com/dpryan79/MethylDackel/blob/master/README.md licence: ["MIT"] + identifier: biotools:methyldackel input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file - pattern: "*.{fasta,fa}" - - fai: - type: file - description: FASTA index file - pattern: "*.{fai}" - - bam: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - bai: - type: file - description: BAM/CRAM index file - pattern: "*.{bai,crai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - bai: + type: file + description: BAM/CRAM index file + pattern: "*.{bai,crai}" + - - fasta: + type: file + description: Input genome fasta file + pattern: "*.{fasta,fa}" + - - fai: + type: file + description: FASTA index file + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - txt: - type: file - description: Text file containing methylation bias - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mbias.txt": + type: file + description: Text file containing methylation bias + pattern: "*.{txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" +maintainers: + - "@phue" diff --git a/modules/nf-core/methyldackel/mbias/nextflow.config b/modules/nf-core/methyldackel/mbias/nextflow.config new file mode 100644 index 00000000..8ae58f00 --- /dev/null +++ b/modules/nf-core/methyldackel/mbias/nextflow.config @@ -0,0 +1,15 @@ +process { + withName: METHYLDACKEL_MBIAS { + ext.args = [ + params.comprehensive ? ' --CHG --CHH' : '', + params.ignore_flags ? " --ignoreFlags" : '' + ].join(" ").trim() + publishDir = [ + [ + path: { "${params.outdir}/methyldackel/mbias" }, + mode: params.publish_dir_mode, + pattern: "*mbias.txt" + ] + ] + } +} \ No newline at end of file diff --git a/modules/nf-core/methyldackel/mbias/tests/main.nf.test b/modules/nf-core/methyldackel/mbias/tests/main.nf.test new file mode 100644 index 00000000..14c30df7 --- /dev/null +++ b/modules/nf-core/methyldackel/mbias/tests/main.nf.test @@ -0,0 +1,68 @@ + +nextflow_process { + + name "Test Process METHYLDACKEL_MBIAS" + script "../main.nf" + process "METHYLDACKEL_MBIAS" + + tag "modules" + tag "modules_nfcore" + tag "methyldackel" + tag "methyldackel/mbias" + + test("test-methyldackel-mbias") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.txt[0][1]).readLines()[3..7], + process.out.versions + ).match() + } + ) + } + } + + test("test-methyldackel-mbias-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/methyldackel/mbias/tests/main.nf.test.snap b/modules/nf-core/methyldackel/mbias/tests/main.nf.test.snap new file mode 100644 index 00000000..2dc4fde7 --- /dev/null +++ b/modules/nf-core/methyldackel/mbias/tests/main.nf.test.snap @@ -0,0 +1,56 @@ +{ + "test-methyldackel-mbias-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.mbias.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,0d6cea2918112948708bd1c2f5309398" + ], + "txt": [ + [ + { + "id": "test", + "single_end": false + }, + "test.mbias.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,0d6cea2918112948708bd1c2f5309398" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T20:35:24.956573" + }, + "test-methyldackel-mbias": { + "content": [ + [ + "OT\t1\t2\t57\t5", + "OT\t2\t2\t48\t9", + "OT\t1\t3\t37\t5", + "OT\t2\t3\t58\t5", + "OT\t1\t4\t52\t3" + ], + [ + "versions.yml:md5,0d6cea2918112948708bd1c2f5309398" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T20:35:20.084046" + } +} \ No newline at end of file diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index bc0bdb5b..6f5b867b 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,7 +1,5 @@ -name: multiqc channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::multiqc=1.18 + - bioconda::multiqc=1.25.1 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 70708f33..cc0643e1 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,14 +3,16 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.18--pyhdfd78af_0' : - 'biocontainers/multiqc:1.18--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' : + 'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" path(multiqc_config) path(extra_multiqc_config) path(multiqc_logo) + path(replace_names) + path(sample_names) output: path "*multiqc_report.html", emit: report @@ -23,16 +25,22 @@ process MULTIQC { script: def args = task.ext.args ?: '' + def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : '' def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' - def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' + def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : '' + def replace = replace_names ? "--replace-names ${replace_names}" : '' + def samples = sample_names ? "--sample-names ${sample_names}" : '' """ multiqc \\ --force \\ $args \\ $config \\ + $prefix \\ $extra_config \\ $logo \\ + $replace \\ + $samples \\ . cat <<-END_VERSIONS > versions.yml @@ -44,7 +52,7 @@ process MULTIQC { stub: """ mkdir multiqc_data - touch multiqc_plots + mkdir multiqc_plots touch multiqc_report.html cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 45a9bc35..b16c1879 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,5 +1,6 @@ name: multiqc -description: Aggregate results from bioinformatics analyses across many samples into a single report +description: Aggregate results from bioinformatics analyses across many samples into + a single report keywords: - QC - bioinformatics tools @@ -12,40 +13,59 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] + identifier: biotools:multiqc input: - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. - pattern: "*.{yml,yaml}" - - multiqc_logo: - type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" + - - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + - - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + - - extra_multiqc_config: + type: file + description: Second optional config yml for MultiQC. Will override common sections + in multiqc_config. + pattern: "*.{yml,yaml}" + - - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" + - - replace_names: + type: file + description: | + Optional two-column sample renaming file. First column a set of + patterns, second column a set of corresponding replacements. Passed via + MultiQC's `--replace-names` option. + pattern: "*.{tsv}" + - - sample_names: + type: file + description: | + Optional TSV file with headers, passed to the MultiQC --sample_names + argument. + pattern: "*.{tsv}" output: - report: - type: file - description: MultiQC report file - pattern: "multiqc_report.html" + - "*multiqc_report.html": + type: file + description: MultiQC report file + pattern: "multiqc_report.html" - data: - type: directory - description: MultiQC data dir - pattern: "multiqc_data" + - "*_data": + type: directory + description: MultiQC data dir + pattern: "multiqc_data" - plots: - type: file - description: Plots created by MultiQC - pattern: "*_data" + - "*_plots": + type: file + description: Plots created by MultiQC + pattern: "*_data" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@bunop" diff --git a/modules/nf-core/multiqc/nextflow.config b/modules/nf-core/multiqc/nextflow.config new file mode 100644 index 00000000..98cf050f --- /dev/null +++ b/modules/nf-core/multiqc/nextflow.config @@ -0,0 +1,10 @@ +process { + withName: 'MULTIQC' { + ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } + publishDir = [ + path: { "${params.outdir}/multiqc/${params.aligner}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } +} \ No newline at end of file diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index d0438eda..33316a7d 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -3,19 +3,24 @@ nextflow_process { name "Test Process MULTIQC" script "../main.nf" process "MULTIQC" + tag "modules" tag "modules_nfcore" tag "multiqc" + config "./nextflow.config" + test("sarscov2 single-end [fastqc]") { when { process { """ - input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -25,7 +30,7 @@ nextflow_process { { assert process.success }, { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("multiqc_versions_single") } ) } @@ -36,10 +41,12 @@ nextflow_process { when { process { """ - input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -49,7 +56,7 @@ nextflow_process { { assert process.success }, { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("multiqc_versions_config") } ) } } @@ -61,10 +68,12 @@ nextflow_process { when { process { """ - input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -75,7 +84,7 @@ nextflow_process { { assert snapshot(process.out.report.collect { file(it).getName() } + process.out.data.collect { file(it).getName() } + process.out.plots.collect { file(it).getName() } + - process.out.versions ).match() } + process.out.versions ).match("multiqc_stub") } ) } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index d087a9df..261dc0fa 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -1,21 +1,41 @@ { - "versions": { + "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,f81e19ab3a8e2b6f2b5d22078117df71" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], - "timestamp": "2023-12-30T00:26:14.048089591" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-02T17:51:46.317523" }, - "sarscov2 single-end [fastqc] - stub": { + "multiqc_stub": { "content": [ [ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,f81e19ab3a8e2b6f2b5d22078117df71" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], - "timestamp": "2023-12-30T00:26:52.963964055" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-02T17:52:20.680978" + }, + "multiqc_versions_config": { + "content": [ + [ + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-02T17:52:09.185842" } -} \ No newline at end of file +} diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config new file mode 100644 index 00000000..c537a6a3 --- /dev/null +++ b/modules/nf-core/multiqc/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'MULTIQC' { + ext.prefix = null + } +} diff --git a/modules/nf-core/picard/markduplicates/environment.yml b/modules/nf-core/picard/markduplicates/environment.yml new file mode 100644 index 00000000..1d715d56 --- /dev/null +++ b/modules/nf-core/picard/markduplicates/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf index 7ba8448f..8a2ed64e 100644 --- a/modules/nf-core/picard/markduplicates/main.nf +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -2,19 +2,20 @@ process PICARD_MARKDUPLICATES { tag "$meta.id" label 'process_medium' - conda "bioconda::picard=3.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' : - 'biocontainers/picard:3.0.0--hdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: - tuple val(meta), path(bam) - path fasta - path fai + tuple val(meta), path(reads) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) output: - tuple val(meta), path("*.bam") , emit: bam - tuple val(meta), path("*.bai") , optional:true, emit: bai + tuple val(meta), path("*.bam") , emit: bam, optional: true + tuple val(meta), path("*.bai") , emit: bai, optional: true + tuple val(meta), path("*.cram"), emit: cram, optional: true tuple val(meta), path("*.metrics.txt"), emit: metrics path "versions.yml" , emit: versions @@ -24,20 +25,25 @@ process PICARD_MARKDUPLICATES { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" + def suffix = task.ext.suffix ?: "${reads.getExtension()}" + def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" def avail_mem = 3072 if (!task.memory) { log.info '[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { avail_mem = (task.memory.mega*0.8).intValue() } + + if ("$reads" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ picard \\ -Xmx${avail_mem}M \\ MarkDuplicates \\ $args \\ - --INPUT $bam \\ - --OUTPUT ${prefix}.bam \\ - --REFERENCE_SEQUENCE $fasta \\ + --INPUT $reads \\ + --OUTPUT ${prefix}.${suffix} \\ + $reference \\ --METRICS_FILE ${prefix}.MarkDuplicates.metrics.txt cat <<-END_VERSIONS > versions.yml @@ -48,9 +54,10 @@ process PICARD_MARKDUPLICATES { stub: def prefix = task.ext.prefix ?: "${meta.id}" + def suffix = task.ext.suffix ?: "${reads.getExtension()}" + if ("$reads" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ - touch ${prefix}.bam - touch ${prefix}.bam.bai + touch ${prefix}.${suffix} touch ${prefix}.MarkDuplicates.metrics.txt cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/picard/markduplicates/meta.yml b/modules/nf-core/picard/markduplicates/meta.yml index 3f2357bb..bcaf9160 100644 --- a/modules/nf-core/picard/markduplicates/meta.yml +++ b/modules/nf-core/picard/markduplicates/meta.yml @@ -15,46 +15,87 @@ tools: homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/ licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam,cram,sam}" - - fasta: - type: file - description: Reference genome fasta file - pattern: "*.{fasta,fa}" - - fai: - type: file - description: Reference genome fasta index - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Sequence reads file, can be SAM/BAM/CRAM format + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome fasta file, required for CRAM input + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Reference genome fasta index + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: BAM file with duplicate reads marked/removed - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: BAM file with duplicate reads marked/removed + pattern: "*.{bam}" - bai: - type: file - description: An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag - pattern: "*.{bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: An optional BAM index file. If desired, --CREATE_INDEX must be + passed as a flag + pattern: "*.{bai}" + - cram: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Output CRAM file + pattern: "*.{cram}" - metrics: - type: file - description: Duplicate metrics file generated by picard - pattern: "*.{metrics.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.metrics.txt": + type: file + description: Duplicate metrics file generated by picard + pattern: "*.{metrics.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@projectoriented" + - "@ramprasadn" +maintainers: + - "@drpatelh" + - "@projectoriented" + - "@ramprasadn" diff --git a/modules/nf-core/picard/markduplicates/nextflow.config b/modules/nf-core/picard/markduplicates/nextflow.config new file mode 100644 index 00000000..1c3c2ec7 --- /dev/null +++ b/modules/nf-core/picard/markduplicates/nextflow.config @@ -0,0 +1,18 @@ +process { + withName: PICARD_MARKDUPLICATES { + ext.args = "--ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --PROGRAM_RECORD_ID 'null' --TMP_DIR tmp" + ext.prefix = { "${meta.id}.markdup.sorted" } + publishDir = [ + [ + path: { "${params.outdir}/${params.aligner}/deduplicated/picard_metrics" }, + pattern: "*.metrics.txt", + mode: params.publish_dir_mode + ], + [ + path: { "${params.outdir}/${params.aligner}/deduplicated" }, + pattern: "*.bam", + mode: params.publish_dir_mode + ] + ] + } +} \ No newline at end of file diff --git a/modules/nf-core/picard/markduplicates/tests/main.nf.test b/modules/nf-core/picard/markduplicates/tests/main.nf.test new file mode 100644 index 00000000..9ed90965 --- /dev/null +++ b/modules/nf-core/picard/markduplicates/tests/main.nf.test @@ -0,0 +1,173 @@ +nextflow_process { + + name "Test Process PICARD_MARKDUPLICATES" + script "../main.nf" + process "PICARD_MARKDUPLICATES" + config "./nextflow.config" + tag "modules" + tag "modules_nfcore" + tag "picard" + tag "picard/markduplicates" + + test("sarscov2 [unsorted bam]") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ]) + input[1] = [ [:], [] ] + input[2] = [ [:], [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.bam[0][1]).name, + path(process.out.metrics.get(0).get(1)).readLines()[0..2], + process.out.versions) + .match() } + ) + } + } + + test("sarscov2 [sorted bam]") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + input[1] = [ [:], [] ] + input[2] = [ [:], [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.bam[0][1]).name, + path(process.out.metrics.get(0).get(1)).readLines()[0..2], + process.out.versions) + .match() } + ) + } + } + + test("homo_sapiens [cram]") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.cram[0][1]).name, + path(process.out.metrics.get(0).get(1)).readLines()[0..2], + process.out.versions) + .match() } + ) + } + } + + test("sarscov2 [unsorted bam] - stub") { + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ]) + input[1] = [ [:], [] ] + input[2] = [ [:], [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 [sorted bam] - stub") { + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + input[1] = [ [:], [] ] + input[2] = [ [:], [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("homo_sapiens [cram] - stub") { + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap new file mode 100644 index 00000000..13770a8e --- /dev/null +++ b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap @@ -0,0 +1,251 @@ +{ + "sarscov2 [sorted bam] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.marked.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" + ], + "bai": [ + + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.marked.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "cram": [ + + ], + "metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T10:58:50.046420643" + }, + "sarscov2 [unsorted bam] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.marked.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" + ], + "bai": [ + + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.marked.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "cram": [ + + ], + "metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T10:58:36.738907079" + }, + "sarscov2 [unsorted bam]": { + "content": [ + "test.marked.bam", + [ + "## htsjdk.samtools.metrics.StringHeader", + "# MarkDuplicates --INPUT test.paired_end.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "## htsjdk.samtools.metrics.StringHeader" + ], + [ + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T10:57:16.683233382" + }, + "sarscov2 [sorted bam]": { + "content": [ + "test.marked.bam", + [ + "## htsjdk.samtools.metrics.StringHeader", + "# MarkDuplicates --INPUT test.paired_end.sorted.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "## htsjdk.samtools.metrics.StringHeader" + ], + [ + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T10:57:47.416956759" + }, + "homo_sapiens [cram]": { + "content": [ + "test.marked.cram", + [ + "## htsjdk.samtools.metrics.StringHeader", + "# MarkDuplicates --INPUT test.paired_end.sorted.cram --OUTPUT test.marked.cram --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "## htsjdk.samtools.metrics.StringHeader" + ], + [ + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T10:58:15.143314223" + }, + "homo_sapiens [cram] - stub": { + "content": [ + { + "0": [ + + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.marked.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" + ], + "bai": [ + + ], + "bam": [ + + ], + "cram": [ + [ + { + "id": "test", + "single_end": false + }, + "test.marked.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T10:59:03.402916523" + } +} \ No newline at end of file diff --git a/modules/nf-core/picard/markduplicates/tests/nextflow.config b/modules/nf-core/picard/markduplicates/tests/nextflow.config new file mode 100644 index 00000000..02818dd6 --- /dev/null +++ b/modules/nf-core/picard/markduplicates/tests/nextflow.config @@ -0,0 +1,6 @@ +process { + withName: PICARD_MARKDUPLICATES { + ext.prefix = { "${meta.id}.marked" } + ext.args = '--ASSUME_SORT_ORDER queryname' + } +} diff --git a/modules/nf-core/picard/markduplicates/tests/tags.yml b/modules/nf-core/picard/markduplicates/tests/tags.yml new file mode 100644 index 00000000..4f213d62 --- /dev/null +++ b/modules/nf-core/picard/markduplicates/tests/tags.yml @@ -0,0 +1,2 @@ +picard/markduplicates: + - modules/nf-core/picard/markduplicates/** diff --git a/modules/nf-core/preseq/lcextrap/environment.yml b/modules/nf-core/preseq/lcextrap/environment.yml new file mode 100644 index 00000000..6300d3f3 --- /dev/null +++ b/modules/nf-core/preseq/lcextrap/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::preseq=3.2.0 diff --git a/modules/nf-core/preseq/lcextrap/main.nf b/modules/nf-core/preseq/lcextrap/main.nf index 12546f0a..540a5fb2 100644 --- a/modules/nf-core/preseq/lcextrap/main.nf +++ b/modules/nf-core/preseq/lcextrap/main.nf @@ -1,12 +1,12 @@ process PRESEQ_LCEXTRAP { tag "$meta.id" label 'process_single' - label 'error_ignore' + label 'error_retry' - conda "bioconda::preseq=3.1.2" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/preseq:3.1.2--h445547b_2': - 'biocontainers/preseq:3.1.2--h445547b_2' }" + 'https://depot.galaxyproject.org/singularity/preseq:3.2.0--hdcf5f25_6': + 'biocontainers/preseq:3.2.0--hdcf5f25_6' }" input: tuple val(meta), path(bam) @@ -21,6 +21,7 @@ process PRESEQ_LCEXTRAP { script: def args = task.ext.args ?: '' + args = task.attempt > 1 ? args.join(' -defects') : args // Disable testing for defects def prefix = task.ext.prefix ?: "${meta.id}" def paired_end = meta.single_end ? '' : '-pe' """ @@ -37,4 +38,16 @@ process PRESEQ_LCEXTRAP { preseq: \$(echo \$(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.lc_extrap.txt + touch ${prefix}.command.log + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + preseq: \$(echo \$(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/preseq/lcextrap/meta.yml b/modules/nf-core/preseq/lcextrap/meta.yml old mode 100755 new mode 100644 index 1391961c..28fb449c --- a/modules/nf-core/preseq/lcextrap/meta.yml +++ b/modules/nf-core/preseq/lcextrap/meta.yml @@ -1,48 +1,58 @@ name: preseq_lcextrap -description: Software for predicting library complexity and genome coverage in high-throughput sequencing +description: Software for predicting library complexity and genome coverage in high-throughput + sequencing keywords: - preseq - library - complexity tools: - preseq: - description: Software for predicting library complexity and genome coverage in high-throughput sequencing + description: Software for predicting library complexity and genome coverage in + high-throughput sequencing homepage: http://smithlabresearch.org/software/preseq/ documentation: http://smithlabresearch.org/wp-content/uploads/manual.pdf tool_dev_url: https://github.com/smithlabcode/preseq - licence: ["GPL"] - + identifier: biotools:preseq input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - lc_extrap: - type: file - description: File containing output of Preseq lcextrap - pattern: "*.{lc_extrap.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.lc_extrap.txt": + type: file + description: File containing output of Preseq lcextrap + pattern: "*.{lc_extrap.txt}" - log: - type: file - description: Log file containing stderr produced by Preseq - pattern: "*.{log}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file containing stderr produced by Preseq + pattern: "*.{log}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - - "@Emiller88" + - "@edmundmiller" +maintainers: + - "@drpatelh" + - "@edmundmiller" diff --git a/modules/nf-core/preseq/lcextrap/nextflow.config b/modules/nf-core/preseq/lcextrap/nextflow.config new file mode 100644 index 00000000..827ef5ed --- /dev/null +++ b/modules/nf-core/preseq/lcextrap/nextflow.config @@ -0,0 +1,17 @@ +process { + withName: PRESEQ_LCEXTRAP { + ext.args = " -verbose -bam" + publishDir = [ + [ + path: { "${params.outdir}/${params.aligner}/preseq" }, + mode: params.publish_dir_mode, + pattern: "*.txt" + ], + [ + path: { "${params.outdir}/${params.aligner}/preseq/log" }, + mode: params.publish_dir_mode, + pattern: "*.log" + ] + ] + } +} \ No newline at end of file diff --git a/modules/nf-core/preseq/lcextrap/tests/main.nf.test b/modules/nf-core/preseq/lcextrap/tests/main.nf.test new file mode 100644 index 00000000..d1af1f0e --- /dev/null +++ b/modules/nf-core/preseq/lcextrap/tests/main.nf.test @@ -0,0 +1,100 @@ +nextflow_process { + + name "Test Process PRESEQ_LCEXTRAP" + script "../main.nf" + process "PRESEQ_LCEXTRAP" + tag "modules" + tag "modules_nfcore" + tag "preseq" + tag "preseq/lcextrap" + + test("sarscov2 - single_end") { + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'delete_me/preseq/SRR1003759_5M_subset.mr', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.log[0][1]).name).match("single_end - log") }, + { assert snapshot(process.out.lc_extrap).match("single_end - lc_extrap") }, + { assert snapshot(process.out.versions).match("single_end - versions") } + ) + } + } + + test("sarscov2 - single_end - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'delete_me/preseq/SRR1003759_5M_subset.mr', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 - paired_end") { + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'delete_me/preseq/SRR1003759_5M_subset.mr', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.log[0][1]).name).match("paired_end - log") }, + { assert snapshot(process.out.lc_extrap).match("paired_end - lc_extrap") }, + { assert snapshot(process.out.versions).match("paired_end - versions") } + ) + } + } + + test("sarscov2 - paired_end - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'delete_me/preseq/SRR1003759_5M_subset.mr', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/preseq/lcextrap/tests/main.nf.test.snap b/modules/nf-core/preseq/lcextrap/tests/main.nf.test.snap new file mode 100644 index 00000000..c725d8e8 --- /dev/null +++ b/modules/nf-core/preseq/lcextrap/tests/main.nf.test.snap @@ -0,0 +1,188 @@ +{ + "single_end - lc_extrap": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.lc_extrap.txt:md5,1fa5cdd601079329618f61660bee00de" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2023-11-23T17:20:40.735535" + }, + "paired_end - log": { + "content": [ + "test.command.log" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2023-11-23T17:20:51.981746" + }, + "single_end - versions": { + "content": [ + [ + "versions.yml:md5,e099c02ff6a63c1dacc6c79fd3d0223e" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-19T16:55:55.821665692" + }, + "sarscov2 - single_end - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.lc_extrap.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.command.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e099c02ff6a63c1dacc6c79fd3d0223e" + ], + "lc_extrap": [ + [ + { + "id": "test", + "single_end": true + }, + "test.lc_extrap.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "log": [ + [ + { + "id": "test", + "single_end": true + }, + "test.command.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e099c02ff6a63c1dacc6c79fd3d0223e" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-19T16:56:11.779385911" + }, + "paired_end - versions": { + "content": [ + [ + "versions.yml:md5,e099c02ff6a63c1dacc6c79fd3d0223e" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-19T16:56:31.353046182" + }, + "single_end - log": { + "content": [ + "test.command.log" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2023-11-23T17:20:40.72985" + }, + "paired_end - lc_extrap": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.lc_extrap.txt:md5,10e5ea860e87fb6f5dc10f4f20c62040" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2023-11-23T17:20:51.998533" + }, + "sarscov2 - paired_end - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.lc_extrap.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.command.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e099c02ff6a63c1dacc6c79fd3d0223e" + ], + "lc_extrap": [ + [ + { + "id": "test", + "single_end": false + }, + "test.lc_extrap.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "log": [ + [ + { + "id": "test", + "single_end": false + }, + "test.command.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e099c02ff6a63c1dacc6c79fd3d0223e" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-19T16:56:45.034808313" + } +} \ No newline at end of file diff --git a/modules/nf-core/preseq/lcextrap/tests/tags.yml b/modules/nf-core/preseq/lcextrap/tests/tags.yml new file mode 100644 index 00000000..b9e25ea7 --- /dev/null +++ b/modules/nf-core/preseq/lcextrap/tests/tags.yml @@ -0,0 +1,2 @@ +preseq/lcextrap: + - modules/nf-core/preseq/lcextrap/** diff --git a/modules/nf-core/qualimap/bamqc/environment.yml b/modules/nf-core/qualimap/bamqc/environment.yml new file mode 100644 index 00000000..4fa5f4e8 --- /dev/null +++ b/modules/nf-core/qualimap/bamqc/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::qualimap=2.3 diff --git a/modules/nf-core/qualimap/bamqc/main.nf b/modules/nf-core/qualimap/bamqc/main.nf index fef7307a..8140e143 100644 --- a/modules/nf-core/qualimap/bamqc/main.nf +++ b/modules/nf-core/qualimap/bamqc/main.nf @@ -2,10 +2,10 @@ process QUALIMAP_BAMQC { tag "$meta.id" label 'process_medium' - conda "bioconda::qualimap=2.2.2d" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1' : - 'biocontainers/qualimap:2.2.2d--1' }" + 'https://depot.galaxyproject.org/singularity/qualimap:2.3--hdfd78af_0' : + 'biocontainers/qualimap:2.3--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/qualimap/bamqc/meta.yml b/modules/nf-core/qualimap/bamqc/meta.yml index 303532eb..8be33c00 100644 --- a/modules/nf-core/qualimap/bamqc/meta.yml +++ b/modules/nf-core/qualimap/bamqc/meta.yml @@ -15,33 +15,38 @@ tools: documentation: http://qualimap.conesalab.org/doc_html/index.html doi: 10.1093/bioinformatics/bts503 licence: ["GPL-2.0-only"] + identifier: biotools:qualimap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam}" - - gff: - type: file - description: Feature file with regions of interest - pattern: "*.{gff,gtf,bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" + - - gff: + type: file + description: Feature file with regions of interest + pattern: "*.{gff,gtf,bed}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - results: - type: dir - description: Qualimap results dir - pattern: "*/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: directory + description: Qualimap results dir + pattern: "*/*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" +maintainers: + - "@phue" diff --git a/modules/nf-core/qualimap/bamqc/nextflow.config b/modules/nf-core/qualimap/bamqc/nextflow.config new file mode 100644 index 00000000..004b4047 --- /dev/null +++ b/modules/nf-core/qualimap/bamqc/nextflow.config @@ -0,0 +1,8 @@ +process { + withName: QUALIMAP_BAMQC { + ext.args = [ + params.genome.toString().startsWith('GRCh') ? '-gd HUMAN' : '', + params.genome.toString().startsWith('GRCm') ? '-gd MOUSE' : '' + ].join(" ").trim() + } +} \ No newline at end of file diff --git a/modules/nf-core/qualimap/bamqc/tests/main.nf.test b/modules/nf-core/qualimap/bamqc/tests/main.nf.test new file mode 100644 index 00000000..eec1a41a --- /dev/null +++ b/modules/nf-core/qualimap/bamqc/tests/main.nf.test @@ -0,0 +1,61 @@ +nextflow_process { + + name "Test Process QUALIMAP_BAMQC" + script "../main.nf" + process "QUALIMAP_BAMQC" + tag "modules" + tag "modules_nfcore" + tag "qualimap" + tag "qualimap/bamqc" + + test("homo_sapiens [bam]") { + when { + process { + """ + gff = [] + + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + input[1] = gff + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + file("${process.out.results[0][1]}/qualimapReport.html").name, + path("${process.out.results[0][1]}/genome_results.txt"), + process.out.versions) + .match() } + ) + } + } + + test("homo_sapiens [bam] - stub") { + options "-stub" + when { + process { + """ + gff = [] + + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + input[1] = gff + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/qualimap/bamqc/tests/main.nf.test.snap b/modules/nf-core/qualimap/bamqc/tests/main.nf.test.snap new file mode 100644 index 00000000..fb6e23e4 --- /dev/null +++ b/modules/nf-core/qualimap/bamqc/tests/main.nf.test.snap @@ -0,0 +1,165 @@ +{ + "homo_sapiens [bam] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + [ + 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"0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T12:27:15.04081" + }, + "homo_sapiens [bam]": { + "content": [ + "qualimapReport.html", + "genome_results.txt:md5,45103d63ba82df2b905eb04819c32dd3", + [ + "versions.yml:md5,9024d7d0a189d8be1485249ae591b907" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:21:02.541915" + } +} \ No newline at end of file diff --git a/modules/nf-core/qualimap/bamqc/tests/tags.yml b/modules/nf-core/qualimap/bamqc/tests/tags.yml new file mode 100644 index 00000000..b2b5eb6f --- /dev/null +++ b/modules/nf-core/qualimap/bamqc/tests/tags.yml @@ -0,0 +1,2 @@ +qualimap/bamqc: + - modules/nf-core/qualimap/bamqc/** diff --git a/modules/nf-core/qualimap/bamqccram/environment.yml b/modules/nf-core/qualimap/bamqccram/environment.yml new file mode 100644 index 00000000..609b5f74 --- /dev/null +++ b/modules/nf-core/qualimap/bamqccram/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::qualimap=2.2.2d + - bioconda::samtools=1.16.1 diff --git a/modules/nf-core/qualimap/bamqccram/main.nf b/modules/nf-core/qualimap/bamqccram/main.nf index 327d8557..81e1a485 100644 --- a/modules/nf-core/qualimap/bamqccram/main.nf +++ b/modules/nf-core/qualimap/bamqccram/main.nf @@ -2,7 +2,7 @@ process QUALIMAP_BAMQCCRAM { tag "$meta.id" label 'process_medium' - conda "bioconda::qualimap=2.2.2d bioconda::samtools=1.16.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:00d3c18496ddf07ea580fd00d1dd203cf31ab630-0' : 'biocontainers/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:00d3c18496ddf07ea580fd00d1dd203cf31ab630-0' }" @@ -57,4 +57,16 @@ process QUALIMAP_BAMQCCRAM { samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + """ + mkdir ${prefix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//') + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/qualimap/bamqccram/meta.yml b/modules/nf-core/qualimap/bamqccram/meta.yml index ea6c4d92..4b7225a5 100644 --- a/modules/nf-core/qualimap/bamqccram/meta.yml +++ b/modules/nf-core/qualimap/bamqccram/meta.yml @@ -15,37 +15,50 @@ tools: documentation: http://qualimap.conesalab.org/doc_html/index.html doi: 10.1093/bioinformatics/bts503 licence: ["GPL-2.0-only"] + identifier: biotools:qualimap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bacramm: - type: file - description: BAM file - pattern: "*.{bam}" - - gff: - type: file - description: Feature file with regions of interest - pattern: "*.{gff,gtf,bed}" - - fasta: - type: file - description: Reference file of cram file - pattern: "*.{fasta,fa,fna}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cram: + type: file + description: Input cram file + pattern: "*.{cram}" + - crai: + type: file + description: Index file for cram file + pattern: "*.{crai}" + - - gff: + type: file + description: Feature file with regions of interest + pattern: "*.{gff,gtf,bed}" + - - fasta: + type: file + description: Reference file of cram file + pattern: "*.{fasta,fa,fna}" + - - fasta_fai: + type: file + description: Index file for reference file + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - results: - type: directory - description: Qualimap results dir - pattern: "*/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: directory + description: Qualimap results dir + pattern: "*/*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" +maintainers: + - "@FriederikeHanssen" diff --git a/modules/nf-core/qualimap/bamqccram/tests/main.nf.test b/modules/nf-core/qualimap/bamqccram/tests/main.nf.test new file mode 100644 index 00000000..da2f300d --- /dev/null +++ b/modules/nf-core/qualimap/bamqccram/tests/main.nf.test @@ -0,0 +1,69 @@ +nextflow_process { + + name "Test Process QUALIMAP_BAMQCCRAM" + script "../main.nf" + process "QUALIMAP_BAMQCCRAM" + tag "modules" + tag "modules_nfcore" + tag "qualimap" + tag "qualimap/bamqccram" + + test("homo_sapiens [cram]") { + when { + process { + """ + gff = [] + + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true) + ]) + input[1] = gff + input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)) + input[3] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + file("${process.out.results[0][1]}/qualimapReport.html").name, + path("${process.out.results[0][1]}/genome_results.txt"), + process.out.versions) + .match() } + ) + } + } + + test("homo_sapiens [cram] - stub") { + + options "-stub" + + when { + process { + """ + gff = [] + + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true) + ]) + input[1] = gff + input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)) + input[3] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/qualimap/bamqccram/tests/main.nf.test.snap b/modules/nf-core/qualimap/bamqccram/tests/main.nf.test.snap new file mode 100644 index 00000000..20b6c4b1 --- /dev/null +++ b/modules/nf-core/qualimap/bamqccram/tests/main.nf.test.snap @@ -0,0 +1,55 @@ +{ + "homo_sapiens [cram]": { + "content": [ + "qualimapReport.html", + "genome_results.txt:md5,61d8b36507652fd7d7db9583de708161", + [ + "versions.yml:md5,9aedcf514cb222dc019feb8b25fc4bcb" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T13:45:35.586664" + }, + "homo_sapiens [cram] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + + ] + ] + ], + "1": [ + "versions.yml:md5,9aedcf514cb222dc019feb8b25fc4bcb" + ], + "results": [ + [ + { + "id": "test", + "single_end": false + }, + [ + + ] + ] + ], + "versions": [ + "versions.yml:md5,9aedcf514cb222dc019feb8b25fc4bcb" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T14:23:41.250873" + } +} \ No newline at end of file diff --git a/modules/nf-core/qualimap/bamqccram/tests/tags.yml b/modules/nf-core/qualimap/bamqccram/tests/tags.yml new file mode 100644 index 00000000..69b06e26 --- /dev/null +++ b/modules/nf-core/qualimap/bamqccram/tests/tags.yml @@ -0,0 +1,2 @@ +qualimap/bamqccram: + - modules/nf-core/qualimap/bamqccram/** diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml new file mode 100644 index 00000000..62054fc9 --- /dev/null +++ b/modules/nf-core/samtools/faidx/environment.yml @@ -0,0 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index 4dd0e5b0..28c0a81c 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -2,18 +2,20 @@ process SAMTOOLS_FAIDX { tag "$fasta" label 'process_single' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(fasta) + tuple val(meta2), path(fai) output: - tuple val(meta), path ("*.fai"), emit: fai - tuple val(meta), path ("*.gzi"), emit: gzi, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path ("*.{fa,fasta}") , emit: fa , optional: true + tuple val(meta), path ("*.fai") , emit: fai, optional: true + tuple val(meta), path ("*.gzi") , emit: gzi, optional: true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -23,8 +25,8 @@ process SAMTOOLS_FAIDX { """ samtools \\ faidx \\ - $args \\ - $fasta + $fasta \\ + $args cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -33,8 +35,12 @@ process SAMTOOLS_FAIDX { """ stub: + def match = (task.ext.args =~ /-o(?:utput)?\s(.*)\s?/).findAll() + def fastacmd = match[0] ? "touch ${match[0][1]}" : '' """ + ${fastacmd} touch ${fasta}.fai + cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml index fe2fe9a1..6721b2cb 100644 --- a/modules/nf-core/samtools/faidx/meta.yml +++ b/modules/nf-core/samtools/faidx/meta.yml @@ -3,6 +3,7 @@ description: Index FASTA file keywords: - index - fasta + - faidx tools: - samtools: description: | @@ -13,35 +14,67 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fa,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fai: + type: file + description: FASTA index file + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - fa: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{fa,fasta}": + type: file + description: FASTA file + pattern: "*.{fa}" - fai: - type: file - description: FASTA index file - pattern: "*.{fai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fai": + type: file + description: FASTA index file + pattern: "*.{fai}" - gzi: - type: file - description: Optional gzip index file for compressed inputs - pattern: "*.gzi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gzi": + type: file + description: Optional gzip index file for compressed inputs + pattern: "*.gzi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" - "@phue" +maintainers: + - "@drpatelh" + - "@ewels" + - "@phue" diff --git a/modules/nf-core/samtools/faidx/nextflow.config b/modules/nf-core/samtools/faidx/nextflow.config new file mode 100644 index 00000000..8b2368a6 --- /dev/null +++ b/modules/nf-core/samtools/faidx/nextflow.config @@ -0,0 +1,11 @@ +process { + withName: SAMTOOLS_FAIDX { + ext.args = "" + publishDir = [ + path: { "${params.outdir}/${params.aligner}/reference_genome" }, + mode: params.publish_dir_mode, + enabled: params.save_reference, + pattern: "*.fai" + ] + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test b/modules/nf-core/samtools/faidx/tests/main.nf.test new file mode 100644 index 00000000..17244ef2 --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test @@ -0,0 +1,122 @@ +nextflow_process { + + name "Test Process SAMTOOLS_FAIDX" + script "../main.nf" + process "SAMTOOLS_FAIDX" + + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/faidx" + + test("test_samtools_faidx") { + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_samtools_faidx_bgzip") { + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)] + + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_samtools_faidx_fasta") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + + input[1] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_samtools_faidx_stub_fasta") { + + config "./nextflow2.config" + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + + input[1] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_samtools_faidx_stub_fai") { + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap new file mode 100644 index 00000000..1bbb3ec2 --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap @@ -0,0 +1,249 @@ +{ + "test_samtools_faidx": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + ], + "fa": [ + + ], + "fai": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "gzi": [ + + ], + "versions": [ + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T07:57:47.450887871" + }, + "test_samtools_faidx_bgzip": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474" + ] + ], + "3": [ + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + ], + "fa": [ + + ], + "fai": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "gzi": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474" + ] + ], + "versions": [ + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T07:58:04.804905659" + }, + "test_samtools_faidx_fasta": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "extract.fa:md5,6a0774a0ad937ba0bfd2ac7457d90f36" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + ], + "fa": [ + [ + { + "id": "test", + "single_end": false + }, + "extract.fa:md5,6a0774a0ad937ba0bfd2ac7457d90f36" + ] + ], + "fai": [ + + ], + "gzi": [ + + ], + "versions": [ + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T07:58:23.831268154" + }, + "test_samtools_faidx_stub_fasta": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "extract.fa:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + ], + "fa": [ + [ + { + "id": "test", + "single_end": false + }, + "extract.fa:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "fai": [ + + ], + "gzi": [ + + ], + "versions": [ + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T07:58:35.600243706" + }, + "test_samtools_faidx_stub_fai": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + ], + "fa": [ + + ], + "fai": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "gzi": [ + + ], + "versions": [ + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T07:58:54.705460167" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/faidx/tests/nextflow.config b/modules/nf-core/samtools/faidx/tests/nextflow.config new file mode 100644 index 00000000..f76a3ba0 --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: SAMTOOLS_FAIDX { + ext.args = 'MT192765.1 -o extract.fa' + } + +} diff --git a/modules/nf-core/samtools/faidx/tests/nextflow2.config b/modules/nf-core/samtools/faidx/tests/nextflow2.config new file mode 100644 index 00000000..33ebbd5d --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/nextflow2.config @@ -0,0 +1,6 @@ +process { + + withName: SAMTOOLS_FAIDX { + ext.args = '-o extract.fa' + } +} diff --git a/modules/nf-core/samtools/faidx/tests/tags.yml b/modules/nf-core/samtools/faidx/tests/tags.yml new file mode 100644 index 00000000..e4a83948 --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/faidx: + - modules/nf-core/samtools/faidx/** diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml new file mode 100644 index 00000000..62054fc9 --- /dev/null +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -0,0 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index b75707ec..4a499727 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_FLAGSTAT { tag "$meta.id" label 'process_single' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/flagstat/meta.yml b/modules/nf-core/samtools/flagstat/meta.yml index 954225df..cdc4c254 100644 --- a/modules/nf-core/samtools/flagstat/meta.yml +++ b/modules/nf-core/samtools/flagstat/meta.yml @@ -1,5 +1,6 @@ name: samtools_flagstat -description: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type +description: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG + type keywords: - stats - mapping @@ -17,33 +18,38 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: Index for BAM/CRAM/SAM file - pattern: "*.{bai,crai,sai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: Index for BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - flagstat: - type: file - description: File containing samtools flagstat output - pattern: "*.{flagstat}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.flagstat": + type: file + description: File containing samtools flagstat output + pattern: "*.{flagstat}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" +maintainers: + - "@drpatelh" diff --git a/modules/nf-core/samtools/flagstat/nextflow.config b/modules/nf-core/samtools/flagstat/nextflow.config new file mode 100644 index 00000000..2cf4ca87 --- /dev/null +++ b/modules/nf-core/samtools/flagstat/nextflow.config @@ -0,0 +1,11 @@ +process { + withName: SAMTOOLS_FLAGSTAT { + publishDir = [ + [ + path: { "${params.outdir}/${params.aligner}/alignments/samtools_stats/" }, + mode: params.publish_dir_mode, + pattern: "*.flagstat" + ] + ] + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test b/modules/nf-core/samtools/flagstat/tests/main.nf.test new file mode 100644 index 00000000..3b648a37 --- /dev/null +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test @@ -0,0 +1,56 @@ +nextflow_process { + + name "Test Process SAMTOOLS_FLAGSTAT" + script "../main.nf" + process "SAMTOOLS_FLAGSTAT" + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/flagstat" + + test("BAM") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("BAM - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap new file mode 100644 index 00000000..04c3852b --- /dev/null +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "BAM - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" + ], + "flagstat": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T08:02:58.866491759" + }, + "BAM": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" + ] + ], + "1": [ + "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" + ], + "flagstat": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" + ] + ], + "versions": [ + "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T08:02:47.383332837" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/flagstat/tests/tags.yml b/modules/nf-core/samtools/flagstat/tests/tags.yml new file mode 100644 index 00000000..2d2b7255 --- /dev/null +++ b/modules/nf-core/samtools/flagstat/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/flagstat: + - modules/nf-core/samtools/flagstat/** diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml new file mode 100644 index 00000000..62054fc9 --- /dev/null +++ b/modules/nf-core/samtools/index/environment.yml @@ -0,0 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 0b20aa4b..31175610 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_INDEX { tag "$meta.id" label 'process_low' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input) @@ -35,10 +35,11 @@ process SAMTOOLS_INDEX { """ stub: + def args = task.ext.args ?: '' + def extension = file(input).getExtension() == 'cram' ? + "crai" : args.contains("-c") ? "csi" : "bai" """ - touch ${input}.bai - touch ${input}.crai - touch ${input}.csi + touch ${input}.${extension} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml index 8bd2fa6f..db8df0d5 100644 --- a/modules/nf-core/samtools/index/meta.yml +++ b/modules/nf-core/samtools/index/meta.yml @@ -15,39 +15,57 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: input file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bai: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" - - crai: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" - csi: - type: file - description: CSI index file - pattern: "*.{csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: CSI index file + pattern: "*.{csi}" + - crai: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" - "@maxulysse" +maintainers: + - "@drpatelh" + - "@ewels" + - "@maxulysse" diff --git a/modules/nf-core/samtools/index/tests/csi.nextflow.config b/modules/nf-core/samtools/index/tests/csi.nextflow.config new file mode 100644 index 00000000..0ed260ef --- /dev/null +++ b/modules/nf-core/samtools/index/tests/csi.nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: SAMTOOLS_INDEX { + ext.args = '-c' + } + +} diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test new file mode 100644 index 00000000..ca34fb5c --- /dev/null +++ b/modules/nf-core/samtools/index/tests/main.nf.test @@ -0,0 +1,140 @@ +nextflow_process { + + name "Test Process SAMTOOLS_INDEX" + script "../main.nf" + process "SAMTOOLS_INDEX" + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/index" + + test("bai") { + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("crai") { + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("csi") { + config "./csi.nextflow.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + file(process.out.csi[0][1]).name, + process.out.versions + ).match() } + ) + } + } + + test("bai - stub") { + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("crai - stub") { + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("csi - stub") { + options "-stub" + config "./csi.nextflow.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap new file mode 100644 index 00000000..72d65e81 --- /dev/null +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -0,0 +1,250 @@ +{ + "csi - stub": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + ], + "bai": [ + + ], + "crai": [ + + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T08:21:25.261127166" + }, + "crai - stub": { + "content": [ + { + "0": [ + + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + ], + "bai": [ + + ], + "crai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T08:21:12.653194876" + }, + "bai - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + ], + "bai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "crai": [ + + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T08:21:01.854932651" + }, + "csi": { + "content": [ + "test.paired_end.sorted.bam.csi", + [ + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T08:20:51.485364222" + }, + "crai": { + "content": [ + { + "0": [ + + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + ] + ], + "3": [ + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + ], + "bai": [ + + ], + "crai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + ] + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T08:20:40.518873972" + }, + "bai": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + ], + "bai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" + ] + ], + "crai": [ + + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T08:20:21.184050361" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/index/tests/tags.yml b/modules/nf-core/samtools/index/tests/tags.yml new file mode 100644 index 00000000..e0f58a7a --- /dev/null +++ b/modules/nf-core/samtools/index/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/index: + - modules/nf-core/samtools/index/** diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml new file mode 100644 index 00000000..62054fc9 --- /dev/null +++ b/modules/nf-core/samtools/sort/environment.yml @@ -0,0 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 2b7753fd..caf3c61a 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -2,18 +2,21 @@ process SAMTOOLS_SORT { tag "$meta.id" label 'process_medium' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: - tuple val(meta), path(bam) + tuple val(meta) , path(bam) + tuple val(meta2), path(fasta) output: - tuple val(meta), path("*.bam"), emit: bam - tuple val(meta), path("*.csi"), emit: csi, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("*.bam"), emit: bam, optional: true + tuple val(meta), path("*.cram"), emit: cram, optional: true + tuple val(meta), path("*.crai"), emit: crai, optional: true + tuple val(meta), path("*.csi"), emit: csi, optional: true + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when @@ -21,14 +24,23 @@ process SAMTOOLS_SORT { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" + def extension = args.contains("--output-fmt sam") ? "sam" : + args.contains("--output-fmt cram") ? "cram" : + "bam" + def reference = fasta ? "--reference ${fasta}" : "" if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + samtools cat \\ + ${bam} \\ + | \\ samtools sort \\ $args \\ - -@ $task.cpus \\ - -o ${prefix}.bam \\ - -T $prefix \\ - $bam + -T ${prefix} \\ + --threads $task.cpus \\ + ${reference} \\ + -o ${prefix}.${extension} \\ + - cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -37,9 +49,20 @@ process SAMTOOLS_SORT { """ stub: + def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" + def extension = args.contains("--output-fmt sam") ? "sam" : + args.contains("--output-fmt cram") ? "cram" : + "bam" """ - touch ${prefix}.bam + touch ${prefix}.${extension} + if [ "${extension}" == "bam" ]; + then + touch ${prefix}.${extension}.csi + elif [ "${extension}" == "cram" ]; + then + touch ${prefix}.${extension}.crai + fi cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml index 07328431..a9dbec5a 100644 --- a/modules/nf-core/samtools/sort/meta.yml +++ b/modules/nf-core/samtools/sort/meta.yml @@ -15,34 +15,78 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file(s) + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fa,fasta,fna}" + optional: true output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Sorted BAM file + pattern: "*.{bam}" + - cram: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Sorted CRAM file + pattern: "*.{cram}" + - crai: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: CRAM index file (optional) + pattern: "*.crai" - csi: - type: file - description: BAM index file (optional) - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: BAM index file (optional) + pattern: "*.csi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" + - "@matthdsm" +maintainers: + - "@drpatelh" + - "@ewels" + - "@matthdsm" diff --git a/modules/nf-core/samtools/sort/nextflow.config b/modules/nf-core/samtools/sort/nextflow.config new file mode 100644 index 00000000..1918458c --- /dev/null +++ b/modules/nf-core/samtools/sort/nextflow.config @@ -0,0 +1,19 @@ +process { + withName: SAMTOOLS_SORT { + ext.prefix = { "${meta.id}.sorted" } + publishDir = [ + [ + path: { "${params.outdir}/${params.aligner}/deduplicated/" }, + mode: params.publish_dir_mode, + pattern: "*markdup*.bam", + enabled: params.save_align_intermeds + ], + [ + path: { "${params.outdir}/${params.aligner}/alignments/" }, + mode: params.publish_dir_mode, + pattern: "*.bam", + enabled: params.save_align_intermeds + ] + ] + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test new file mode 100644 index 00000000..b05e6691 --- /dev/null +++ b/modules/nf-core/samtools/sort/tests/main.nf.test @@ -0,0 +1,192 @@ +nextflow_process { + + name "Test Process SAMTOOLS_SORT" + script "../main.nf" + process "SAMTOOLS_SORT" + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/sort" + + test("bam") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out.bam, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match()} + ) + } + } + + test("multiple bam") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) + ] + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out.bam, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match()} + ) + } + } + + test("cram") { + + config "./nextflow_cram.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out.cram.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.crai.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match()} + ) + } + } + + test("bam - stub") { + + options "-stub" + config "./nextflow.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("multiple bam - stub") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) + ] + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("cram - stub") { + + options "-stub" + config "./nextflow_cram.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap new file mode 100644 index 00000000..469891fe --- /dev/null +++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap @@ -0,0 +1,287 @@ +{ + "cram": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.cram" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.cram.crai" + ] + ], + [ + "versions.yml:md5,2659b187d681241451539d4c53500b9f" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T08:49:58.207549273" + }, + "bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + "versions.yml:md5,2659b187d681241451539d4c53500b9f" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "crai": [ + + ], + "cram": [ + + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,2659b187d681241451539d4c53500b9f" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T08:50:08.630951018" + }, + "cram - stub": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + + ], + "4": [ + "versions.yml:md5,2659b187d681241451539d4c53500b9f" + ], + "bam": [ + + ], + "crai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "cram": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,2659b187d681241451539d4c53500b9f" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T08:50:19.061912443" + }, + "multiple bam": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi" + ] + ], + [ + "versions.yml:md5,2659b187d681241451539d4c53500b9f" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.0" + }, + "timestamp": "2024-10-08T11:59:55.479443" + }, + "multiple bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,d185916eaff9afeb4d0aeab3310371f9" + ] + ], + "4": [ + "versions.yml:md5,2659b187d681241451539d4c53500b9f" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12" + ] + ], + "crai": [ + + ], + "cram": [ + + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,d185916eaff9afeb4d0aeab3310371f9" + ] + ], + "versions": [ + "versions.yml:md5,2659b187d681241451539d4c53500b9f" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.0" + }, + "timestamp": "2024-10-08T11:36:13.781404" + }, + "bam": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,34aa85e86abefe637f7a4a9887f016fc" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi" + ] + ], + [ + "versions.yml:md5,2659b187d681241451539d4c53500b9f" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.0" + }, + "timestamp": "2024-10-08T11:59:46.372244" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/tests/nextflow.config b/modules/nf-core/samtools/sort/tests/nextflow.config new file mode 100644 index 00000000..f642771f --- /dev/null +++ b/modules/nf-core/samtools/sort/tests/nextflow.config @@ -0,0 +1,8 @@ +process { + + withName: SAMTOOLS_SORT { + ext.prefix = { "${meta.id}.sorted" } + ext.args = "--write-index" + } + +} diff --git a/modules/nf-core/samtools/sort/tests/nextflow_cram.config b/modules/nf-core/samtools/sort/tests/nextflow_cram.config new file mode 100644 index 00000000..3a8c0188 --- /dev/null +++ b/modules/nf-core/samtools/sort/tests/nextflow_cram.config @@ -0,0 +1,8 @@ +process { + + withName: SAMTOOLS_SORT { + ext.prefix = { "${meta.id}.sorted" } + ext.args = "--write-index --output-fmt cram" + } + +} diff --git a/modules/nf-core/samtools/sort/tests/tags.yml b/modules/nf-core/samtools/sort/tests/tags.yml new file mode 100644 index 00000000..cd63ea20 --- /dev/null +++ b/modules/nf-core/samtools/sort/tests/tags.yml @@ -0,0 +1,3 @@ +samtools/sort: + - modules/nf-core/samtools/sort/** + - tests/modules/nf-core/samtools/sort/** diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml new file mode 100644 index 00000000..62054fc9 --- /dev/null +++ b/modules/nf-core/samtools/stats/environment.yml @@ -0,0 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index eb7f098b..493525a9 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -2,14 +2,14 @@ process SAMTOOLS_STATS { tag "$meta.id" label 'process_single' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input), path(input_index) - path fasta + tuple val(meta2), path(fasta) output: tuple val(meta), path("*.stats"), emit: stats diff --git a/modules/nf-core/samtools/stats/meta.yml b/modules/nf-core/samtools/stats/meta.yml index 1d68a5d8..77b020f7 100644 --- a/modules/nf-core/samtools/stats/meta.yml +++ b/modules/nf-core/samtools/stats/meta.yml @@ -16,38 +16,51 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - fasta: - type: optional file - description: Reference file the CRAM was created with - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference file the CRAM was created with (optional) + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - stats: - type: file - description: File containing samtools stats output - pattern: "*.{stats}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.stats": + type: file + description: File containing samtools stats output + pattern: "*.{stats}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@FriederikeHanssen" + - "@ramprasadn" +maintainers: + - "@drpatelh" + - "@FriederikeHanssen" + - "@ramprasadn" diff --git a/modules/nf-core/samtools/stats/nextflow.config b/modules/nf-core/samtools/stats/nextflow.config new file mode 100644 index 00000000..285e24d7 --- /dev/null +++ b/modules/nf-core/samtools/stats/nextflow.config @@ -0,0 +1,11 @@ +process { + withName: SAMTOOLS_STATS { + publishDir = [ + [ + path: { "${params.outdir}/${params.aligner}/alignments/samtools_stats/" }, + mode: params.publish_dir_mode, + pattern: "*.stats" + ] + ] + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test b/modules/nf-core/samtools/stats/tests/main.nf.test new file mode 100644 index 00000000..5bc89309 --- /dev/null +++ b/modules/nf-core/samtools/stats/tests/main.nf.test @@ -0,0 +1,113 @@ +nextflow_process { + + name "Test Process SAMTOOLS_STATS" + script "../main.nf" + process "SAMTOOLS_STATS" + + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/stats" + + test("bam") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + {assert process.success}, + {assert snapshot(process.out).match()} + ) + } + } + + test("cram") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + {assert process.success}, + {assert snapshot(process.out).match()} + ) + } + } + + test("bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + {assert process.success}, + {assert snapshot(process.out).match()} + ) + } + } + + test("cram - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + {assert process.success}, + {assert snapshot(process.out).match()} + ) + } + } +} diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test.snap b/modules/nf-core/samtools/stats/tests/main.nf.test.snap new file mode 100644 index 00000000..df507be7 --- /dev/null +++ b/modules/nf-core/samtools/stats/tests/main.nf.test.snap @@ -0,0 +1,142 @@ +{ + "cram": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,a27fe55e49a341f92379bb20a65c6a06" + ] + ], + "1": [ + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + ], + "stats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,a27fe55e49a341f92379bb20a65c6a06" + ] + ], + "versions": [ + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T09:29:16.767396182" + }, + "bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + ], + "stats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T09:29:29.721580274" + }, + "cram - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + ], + "stats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T09:29:53.567964304" + }, + "bam": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d53a2584376d78942839e9933a34d11b" + ] + ], + "1": [ + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + ], + "stats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d53a2584376d78942839e9933a34d11b" + ] + ], + "versions": [ + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T09:28:50.73610604" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/stats/tests/tags.yml b/modules/nf-core/samtools/stats/tests/tags.yml new file mode 100644 index 00000000..7c28e30f --- /dev/null +++ b/modules/nf-core/samtools/stats/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/stats: + - modules/nf-core/samtools/stats/** diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml new file mode 100644 index 00000000..910ffa88 --- /dev/null +++ b/modules/nf-core/trimgalore/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda + +dependencies: + - bioconda::cutadapt=4.2 + - bioconda::trim-galore=0.6.10 diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index dcb77ae7..30d17edc 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -2,10 +2,10 @@ process TRIMGALORE { tag "$meta.id" label 'process_high' - conda "bioconda::trim-galore=0.6.7" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0' : - 'biocontainers/trim-galore:0.6.7--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.10--hdfd78af_0' : + 'biocontainers/trim-galore:0.6.10--hdfd78af_0' }" input: tuple val(meta), path(reads) @@ -72,4 +72,25 @@ process TRIMGALORE { END_VERSIONS """ } + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + if (meta.single_end) { + output_command = "echo '' | gzip > ${prefix}_trimmed.fq.gz ;" + output_command += "touch ${prefix}.fastq.gz_trimming_report.txt" + } else { + output_command = "echo '' | gzip > ${prefix}_1_trimmed.fq.gz ;" + output_command += "touch ${prefix}_1.fastq.gz_trimming_report.txt ;" + output_command += "echo '' | gzip > ${prefix}_2_trimmed.fq.gz ;" + output_command += "touch ${prefix}_2.fastq.gz_trimming_report.txt" + } + """ + ${output_command} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//') + cutadapt: \$(cutadapt --version) + END_VERSIONS + """ } diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml index f84c4d77..576cb4c5 100644 --- a/modules/nf-core/trimgalore/meta.yml +++ b/modules/nf-core/trimgalore/meta.yml @@ -14,51 +14,82 @@ tools: homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ documentation: https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: | - List of input adapter trimmed FastQ files of size 1 and 2 for - single-end and paired-end data, respectively. - pattern: "*{3prime,5prime,trimmed,val}*.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*{3prime,5prime,trimmed,val}*.fq.gz": + type: file + description: | + List of input adapter trimmed FastQ files of size 1 and 2 for + single-end and paired-end data, respectively. + pattern: "*{3prime,5prime,trimmed,val}*.fq.gz" + - log: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*report.txt": + type: file + description: Trim Galore! trimming report + pattern: "*_{report.txt}" - unpaired: - type: file - description: | - FastQ files containing unpaired reads from read 1 or read 2 - pattern: "*unpaired*.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*unpaired*.fq.gz": + type: file + description: | + FastQ files containing unpaired reads from read 1 or read 2 + pattern: "*unpaired*.fq.gz" - html: - type: file - description: FastQC report (optional) - pattern: "*_{fastqc.html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: FastQC report (optional) + pattern: "*_{fastqc.html}" - zip: - type: file - description: FastQC report archive (optional) - pattern: "*_{fastqc.zip}" - - log: - type: file - description: Trim Galore! trimming report - pattern: "*_{report.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.zip": + type: file + description: FastQC report archive (optional) + pattern: "*_{fastqc.zip}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" - "@FelixKrueger" +maintainers: + - "@drpatelh" + - "@ewels" + - "@FelixKrueger" diff --git a/modules/nf-core/trimgalore/nextflow.config b/modules/nf-core/trimgalore/nextflow.config new file mode 100644 index 00000000..6c33f5c4 --- /dev/null +++ b/modules/nf-core/trimgalore/nextflow.config @@ -0,0 +1,90 @@ +process { + withName: TRIMGALORE { + ext.args = { [ + // Static args + '--fastqc', + + // Special flags + params.rrbs ? '--rrbs' : '', + params.nextseq_trim > 0 ? "--nextseq ${params.nextseq_trim}" : '', + params.length_trim ? "--length ${params.length_trim}" : '', + + // Trimming - R1 + params.clip_r1 > 0 ? "--clip_r1 ${params.clip_r1}" : ( + params.pbat ? "--clip_r1 9" : ( + (params.single_cell || params.cegx) ? "--clip_r1 6" : ( + params.epignome ? "--clip_r1 8" : ( + (params.accel || params.zymo || params.em_seq) ? "--clip_r1 10" : '' + ) + ) + ) + ), + + // Trimming - R2 + meta.single_end ? '' : ( + params.clip_r2 > 0 ? "--clip_r2 ${params.clip_r2}" : ( + params.pbat ? "--clip_r2 9" : ( + (params.single_cell || params.cegx) ? "--clip_r2 6" : ( + params.epignome ? "--clip_r2 8" : ( + (params.zymo || params.em_seq) ? "--clip_r2 10" : ( + params.accel ? "--clip_r2 15" : '' + ) + ) + ) + ) + ) + ), + + // Trimming - 3' R1 + params.three_prime_clip_r1 > 0 ? "--three_prime_clip_r1 ${params.three_prime_clip_r1}" : ( + params.pbat ? "--three_prime_clip_r1 9" : ( + params.single_cell ? "--three_prime_clip_r1 6" : ( + params.cegx ? "--three_prime_clip_r1 2" : ( + params.epignome ? "--three_prime_clip_r1 8" : ( + (params.accel || params.zymo || params.em_seq) ? "--three_prime_clip_r1 10" : '' + ) + ) + ) + ) + ), + + // Trimming - 3' R2 + meta.single_end ? '' : ( + params.three_prime_clip_r2 > 0 ? "--three_prime_clip_r2 ${params.three_prime_clip_r2}" : ( + params.pbat ? "--three_prime_clip_r2 9" : ( + params.single_cell ? "--three_prime_clip_r2 6" : ( + params.cegx ? "--three_prime_clip_r2 2" : ( + params.epignome ? "--three_prime_clip_r2 8" : ( + (params.accel || params.zymo || params.em_seq) ? "--three_prime_clip_r2 10" : '' + ) + ) + ) + ) + ) + ), + ].join(' ').trim() } + publishDir = [ + [ + path: { "${params.outdir}/trimgalore/fastqc" }, + mode: params.publish_dir_mode, + pattern: "*.html" + ], + [ + path: { "${params.outdir}/trimgalore/fastqc/zips" }, + mode: params.publish_dir_mode, + pattern: "*.zip" + ], + [ + path: { "${params.outdir}/trimgalore" }, + mode: params.publish_dir_mode, + pattern: "*.fq.gz", + enabled: params.save_trimmed + ], + [ + path: { "${params.outdir}/trimgalore/logs" }, + mode: params.publish_dir_mode, + pattern: "*.txt" + ] + ] + } +} \ No newline at end of file diff --git a/modules/nf-core/trimgalore/tests/main.nf.test b/modules/nf-core/trimgalore/tests/main.nf.test new file mode 100644 index 00000000..2a3dbbb0 --- /dev/null +++ b/modules/nf-core/trimgalore/tests/main.nf.test @@ -0,0 +1,150 @@ +nextflow_process { + + name "Test Process TRIMGALORE" + script "../main.nf" + process "TRIMGALORE" + tag "modules" + tag "modules_nfcore" + tag "trimgalore" + + test("test_trimgalore_single_end") { + + when { + process { + """ + input[0] = [ [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ] + ] + """ + } + } + + then { + def read_lines = ["@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1", + "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT", + "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE + { assert path(process.out.reads.get(0).get(1)).linesGzip.contains(read_line) } + } + }, + { report1_lines.each { report1_line -> + { assert path(process.out.log.get(0).get(1)).getText().contains(report1_line) } + } + }, + { assert snapshot(process.out.versions).match() } + ) + } + } + + test("test_trimgalore_single_end - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_trimgalore_paired_end") { + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) + ] + ] + """ + } + } + + then { + def read1_lines = ["@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1", + "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT", + "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE + { assert path(process.out.reads.get(0).get(1).get(0)).linesGzip.contains(read1_line) } + } + }, + { read2_lines.each { read2_line -> + { assert path(process.out.reads.get(0).get(1).get(1)).linesGzip.contains(read2_line) } + } + }, + { report1_lines.each { report1_line -> + { assert path(process.out.log.get(0).get(1).get(0)).getText().contains(report1_line) } + } + }, + { report2_lines.each { report2_line -> + { assert path(process.out.log.get(0).get(1).get(1)).getText().contains(report2_line) } + } + }, + { assert snapshot(process.out.versions).match() } + ) + } + } + + test("test_trimgalore_paired_end - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/trimgalore/tests/main.nf.test.snap b/modules/nf-core/trimgalore/tests/main.nf.test.snap new file mode 100644 index 00000000..61b3504a --- /dev/null +++ b/modules/nf-core/trimgalore/tests/main.nf.test.snap @@ -0,0 +1,180 @@ +{ + "test_trimgalore_single_end": { + "content": [ + [ + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T12:50:36.440264431" + }, + "test_trimgalore_single_end - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test_trimmed.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + + ], + "4": [ + + ], + "5": [ + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" + ], + "html": [ + + ], + "log": [ + [ + { + "id": "test", + "single_end": true + }, + "test.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test_trimmed.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "unpaired": [ + + ], + "versions": [ + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" + ], + "zip": [ + + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T12:50:51.25902234" + }, + "test_trimgalore_paired_end - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1_trimmed.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_2_trimmed.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "2": [ + + ], + "3": [ + + ], + "4": [ + + ], + "5": [ + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" + ], + "html": [ + + ], + "log": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1_trimmed.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_2_trimmed.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "unpaired": [ + + ], + "versions": [ + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" + ], + "zip": [ + + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T12:51:19.024228479" + }, + "test_trimgalore_paired_end": { + "content": [ + [ + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T12:51:02.471703095" + } +} \ No newline at end of file diff --git a/modules/nf-core/trimgalore/tests/tags.yml b/modules/nf-core/trimgalore/tests/tags.yml new file mode 100644 index 00000000..e9937691 --- /dev/null +++ b/modules/nf-core/trimgalore/tests/tags.yml @@ -0,0 +1,2 @@ +trimgalore: + - modules/nf-core/trimgalore/** diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index 2d52ce64..c7794856 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -1,8 +1,7 @@ channels: - conda-forge - bioconda - - defaults dependencies: - - conda-forge::sed=4.7 - conda-forge::grep=3.11 + - conda-forge::sed=4.8 - conda-forge::tar=1.34 diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 8a75bb95..9bd8f554 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -4,8 +4,8 @@ process UNTAR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'nf-core/ubuntu:20.04' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:22.04' : + 'nf-core/ubuntu:22.04' }" input: tuple val(meta), path(archive) @@ -52,8 +52,29 @@ process UNTAR { stub: prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.toString().replaceFirst(/\.[^\.]+(.gz)?$/, "")) """ - mkdir $prefix - touch ${prefix}/file.txt + mkdir ${prefix} + ## Dry-run untaring the archive to get the files and place all in prefix + if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then + for i in `tar -tf ${archive}`; + do + if [[ \$(echo "\${i}" | grep -E "/\$") == "" ]]; + then + touch \${i} + else + mkdir -p \${i} + fi + done + else + for i in `tar -tf ${archive}`; + do + if [[ \$(echo "\${i}" | grep -E "/\$") == "" ]]; + then + touch ${prefix}/\${i} + else + mkdir -p ${prefix}/\${i} + fi + done + fi cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml index a9a2110f..290346b3 100644 --- a/modules/nf-core/untar/meta.yml +++ b/modules/nf-core/untar/meta.yml @@ -10,30 +10,33 @@ tools: Extract tar.gz files. documentation: https://www.gnu.org/software/tar/manual/ licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - archive: - type: file - description: File to be untar - pattern: "*.{tar}.{gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be untar + pattern: "*.{tar}.{gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - untar: - type: directory - description: Directory containing contents of archive - pattern: "*/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - $prefix: + type: directory + description: Directory containing contents of archive + pattern: "*/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test new file mode 100644 index 00000000..c957517a --- /dev/null +++ b/modules/nf-core/untar/tests/main.nf.test @@ -0,0 +1,85 @@ +nextflow_process { + + name "Test Process UNTAR" + script "../main.nf" + process "UNTAR" + tag "modules" + tag "modules_nfcore" + tag "untar" + + test("test_untar") { + + when { + process { + """ + input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } + } + + test("test_untar_onlyfiles") { + + when { + process { + """ + input[0] = [ [], file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } + } + + test("test_untar - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } + } + + test("test_untar_onlyfiles - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ [], file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } + } +} diff --git a/modules/nf-core/untar/tests/main.nf.test.snap b/modules/nf-core/untar/tests/main.nf.test.snap new file mode 100644 index 00000000..ceb91b79 --- /dev/null +++ b/modules/nf-core/untar/tests/main.nf.test.snap @@ -0,0 +1,158 @@ +{ + "test_untar_onlyfiles": { + "content": [ + { + "0": [ + [ + [ + + ], + [ + "hello.txt:md5,e59ff97941044f85df5297e1c302d260" + ] + ] + ], + "1": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ], + "untar": [ + [ + [ + + ], + [ + "hello.txt:md5,e59ff97941044f85df5297e1c302d260" + ] + ] + ], + "versions": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-10T12:04:28.231047" + }, + "test_untar_onlyfiles - stub": { + "content": [ + { + "0": [ + [ + [ + + ], + [ + "hello.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ], + "untar": [ + [ + [ + + ], + [ + "hello.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-10T12:04:45.773103" + }, + "test_untar - stub": { + "content": [ + { + "0": [ + [ + [ + + ], + [ + "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ], + "untar": [ + [ + [ + + ], + [ + "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-10T12:04:36.777441" + }, + "test_untar": { + "content": [ + { + "0": [ + [ + [ + + ], + [ + "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", + "opts.k2d:md5,a033d00cf6759407010b21700938f543", + "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" + ] + ] + ], + "1": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ], + "untar": [ + [ + [ + + ], + [ + "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", + "opts.k2d:md5,a033d00cf6759407010b21700938f543", + "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" + ] + ] + ], + "versions": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-10T12:04:19.377674" + } +} \ No newline at end of file diff --git a/modules/nf-core/untar/tests/tags.yml b/modules/nf-core/untar/tests/tags.yml new file mode 100644 index 00000000..feb6f15c --- /dev/null +++ b/modules/nf-core/untar/tests/tags.yml @@ -0,0 +1,2 @@ +untar: + - modules/nf-core/untar/** diff --git a/nextflow.config b/nextflow.config index d95f12b2..af2a040e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -11,20 +11,19 @@ params { // Input options input = null + // References genome = null igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false - // Qualimap options - bamqc_regions_file = null + // MultiQC options - multiqc_config = null - multiqc_title = null - multiqc_logo = null - max_multiqc_email_size = '25.MB' + multiqc_config = null + multiqc_title = null + multiqc_logo = null + max_multiqc_email_size = '25.MB' multiqc_methods_description = null - // Intermediate files save_reference = false save_align_intermeds = false @@ -35,6 +34,9 @@ params { aligner = 'bismark' comprehensive = false + // Qualimap options + bamqc_regions_file = null + // Library presets pbat = false rrbs = false @@ -52,6 +54,7 @@ params { three_prime_clip_r1 = 0 three_prime_clip_r2 = 0 nextseq_trim = 0 + length_trim = null // Bismark options non_directional = false @@ -85,176 +88,158 @@ params { skip_multiqc = false // Boilerplate options - outdir = null - publish_dir_mode = 'copy' - email = null - email_on_fail = null - plaintext_email = false - monochrome_logs = false - hook_url = null - help = false - version = false + outdir = null + publish_dir_mode = 'copy' + email = null + email_on_fail = null + plaintext_email = false + monochrome_logs = false + hook_url = null + help = false + help_full = false + show_hidden = false + version = false + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/methylseq' // Config options - config_profile_name = null - config_profile_description = null - custom_config_version = 'master' - custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" - config_profile_contact = null - config_profile_url = null - - test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/methylseq" + config_profile_name = null + config_profile_description = null - - // Max resource options - // Defaults only, expecting to be overwritten - max_memory = '128.GB' - max_cpus = 16 - max_time = '240.h' + custom_config_version = 'master' + custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" + config_profile_contact = null + config_profile_url = null // Schema validation default options - validationFailUnrecognisedParams = false - validationLenientMode = false - validationSchemaIgnoreParams = 'genomes,igenomes_base' - validationShowHiddenParams = false - validate_params = true - + validate_params = true } // Load base.config by default for all pipelines includeConfig 'conf/base.config' -// Load nf-core custom profiles from different Institutions -try { - includeConfig "${params.custom_config_base}/nfcore_custom.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") -} - -// Load nf-core/methylseq custom profiles from different institutions. -// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs! -try { - includeConfig "${params.custom_config_base}/pipeline/methylseq.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config/methylseq profiles: ${params.custom_config_base}/pipeline/methylseq.config") -} - profiles { debug { - dumpHashes = true - process.beforeScript = 'echo $HOSTNAME' - cleanup = false + dumpHashes = true + process.beforeScript = 'echo $HOSTNAME' + cleanup = false nextflow.enable.configProcessNamesValidation = true } conda { - conda.enabled = true - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + conda.enabled = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + conda.channels = ['conda-forge', 'bioconda'] + apptainer.enabled = false } mamba { - conda.enabled = true - conda.useMamba = true - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + conda.enabled = true + conda.useMamba = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false } docker { - docker.enabled = true - conda.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false - docker.runOptions = '-u $(id -u):$(id -g)' + docker.enabled = true + conda.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false + docker.runOptions = '-u $(id -u):$(id -g)' } arm { - docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' } singularity { - singularity.enabled = true - singularity.autoMounts = true - conda.enabled = false - docker.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + singularity.enabled = true + singularity.autoMounts = true + conda.enabled = false + docker.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false } podman { - podman.enabled = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + podman.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false } shifter { - shifter.enabled = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - podman.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + shifter.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + charliecloud.enabled = false + apptainer.enabled = false } charliecloud { - charliecloud.enabled = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - apptainer.enabled = false + charliecloud.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + apptainer.enabled = false } apptainer { - apptainer.enabled = true - apptainer.autoMounts = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false + apptainer.enabled = true + apptainer.autoMounts = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + } + wave { + apptainer.ociAutoPull = true + singularity.ociAutoPull = true + wave.enabled = true + wave.freeze = true + wave.strategy = 'conda,container' } gitpod { - executor.name = 'local' - executor.cpus = 4 - executor.memory = 8.GB + executor.name = 'local' + executor.cpus = 4 + executor.memory = 8.GB } test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } - test_ci { params.test_data_base = './test-datasets/' } + test_ci { params.pipelines_testdata_base_path = './test-datasets/' } dev { nextflow.enable.configProcessNamesValidation = true } } -// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile -// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled -// Set to your registry if you have a mirror of containers -apptainer.registry = 'quay.io' -docker.registry = 'quay.io' -podman.registry = 'quay.io' -singularity.registry = 'quay.io' +// Load nf-core custom profiles from different Institutions +includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" -// Nextflow plugins -plugins { - id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet -} +// Load nf-core/methylseq custom profiles from different institutions. +includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/methylseq.config" : "/dev/null" + +// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile +// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled +// Set to your registry if you have a mirror of containers +apptainer.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' +charliecloud.registry = 'quay.io' // Load igenomes.config if required -if (!params.igenomes_ignore) { - includeConfig 'conf/igenomes.config' -} else { - params.genomes = [:] -} +includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config' + // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. @@ -266,8 +251,15 @@ env { JULIA_DEPOT_PATH = "/usr/local/share/julia" } -// Capture exit codes from upstream processes when piping -process.shell = ['/bin/bash', '-euo', 'pipefail'] +// Set bash options +process.shell = """\ +bash + +set -e # Exit if a tool returns a non-zero status/exit code +set -u # Treat unset variables and parameters as an error +set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute +set -C # No clobber - prevent output redirection from overwriting files. +""" // Disable process selector warnings by default. Use debug profile to enable warnings. nextflow.enable.configProcessNamesValidation = false @@ -292,47 +284,50 @@ dag { manifest { name = 'nf-core/methylseq' - author = """Phil Ewels""" + author = """Phil Ewels, Sateesh Peri""" homePage = 'https://github.com/nf-core/methylseq' description = """Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, part of the nf-core community.""" mainScript = 'main.nf' - nextflowVersion = '!>=23.04.0' - version = '2.6.0' + nextflowVersion = '!>=24.04.2' + version = '2.7.0' doi = '10.5281/zenodo.1343417' } -// Load modules.config for DSL2 module specific options -includeConfig 'conf/modules.config' - -// Function to ensure that resource requirements don't go beyond -// a maximum limit -def check_max(obj, type) { - if (type == 'memory') { - try { - if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1) - return params.max_memory as nextflow.util.MemoryUnit - else - return obj - } catch (all) { - println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'time') { - try { - if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1) - return params.max_time as nextflow.util.Duration - else - return obj - } catch (all) { - println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'cpus') { - try { - return Math.min( obj, params.max_cpus as int ) - } catch (all) { - println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj" - return obj - } +// Nextflow plugins +plugins { + id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet +} + +validation { + defaultIgnoreParams = ["genomes"] + help { + enabled = true + command = "nextflow run $manifest.name -profile --input samplesheet.csv --outdir " + fullParameter = "help_full" + showHiddenParameter = "show_hidden" + beforeText = """ +-\033[2m----------------------------------------------------\033[0m- + \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m +\033[0;34m ___ __ __ __ ___ \033[0;32m/,-._.--~\'\033[0m +\033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m +\033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m + \033[0;32m`._,._,\'\033[0m +\033[0;35m ${manifest.name} ${manifest.version}\033[0m +-\033[2m----------------------------------------------------\033[0m- +""" + afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} +* The nf-core framework + https://doi.org/10.1038/s41587-020-0439-x + +* Software dependencies + https://github.com/${manifest.name}/blob/master/CITATIONS.md +""" + } + summary { + beforeText = validation.help.beforeText + afterText = validation.help.afterText } } + +// Load workflow specific config for DSL2 module specific options +includeConfig './workflows/methylseq/nextflow.config' diff --git a/nextflow_schema.json b/nextflow_schema.json index a87bcb95..ca54aada 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/nf-core/methylseq/master/nextflow_schema.json", "title": "nf-core/methylseq pipeline parameters", "description": "Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, part of the nf-core community.", "type": "object", - "definitions": { + "$defs": { "input_output_options": { "title": "Input/output options", "type": "object", @@ -16,9 +16,9 @@ "type": "string", "format": "file-path", "exists": true, + "schema": "assets/schema_input.json", "mimetype": "text/csv", "pattern": "^\\S+\\.csv$", - "schema": "assets/schema_input.json", "description": "Path to comma-separated file containing information about the samples in the experiment.", "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re//usage#samplesheet-input).", "fa_icon": "fas fa-file-csv" @@ -40,13 +40,6 @@ "type": "string", "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.", "fa_icon": "fas fa-file-signature" - }, - "test_data_base": { - "type": "string", - "default": "https://raw.githubusercontent.com/nf-core/test-datasets/methylseq", - "description": "Base path / URL for data used in the test profiles", - "help_text": "Warning: The `-profile test` samplesheet file itself contains remote paths. Setting this parameter does not alter the contents of that file.", - "hidden": true } } }, @@ -118,26 +111,27 @@ "description": "Path to a directory containing a Bismark reference index.", "fa_icon": "fas fa-dot-circle" }, - "bwa_meth_index": { + "bwameth_index": { "type": "string", "format": "path", "description": "bwameth index filename base", "help_text": "Directory for a bwa-meth genome reference index. Only used when using the bwa-meth aligner.\n\nNote that this is not a complete path, but the directory containing the reference. For example, if you have file paths such as `/path/to/ref/genome.fa.bwameth.c2t.bwt`, you should specify `/path/to/ref/`.", "fa_icon": "far fa-dot-circle" }, - "igenomes_base": { - "type": "string", - "description": "Directory / URL base for iGenomes references.", - "default": "s3://ngi-igenomes/igenomes", - "fa_icon": "fas fa-cloud-download-alt", - "hidden": true - }, "igenomes_ignore": { "type": "boolean", "description": "Do not load the iGenomes reference config.", "fa_icon": "fas fa-ban", "hidden": true, "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`." + }, + "igenomes_base": { + "type": "string", + "format": "directory-path", + "description": "The base path to the igenomes reference files", + "fa_icon": "fas fa-ban", + "hidden": true, + "default": "s3://ngi-igenomes/igenomes/" } } }, @@ -262,6 +256,11 @@ "type": "integer", "default": 0, "description": "Trim bases below this quality value from the 3' end of the read, ignoring high-quality G bases" + }, + "length_trim": { + "type": "integer", + "description": "Discard reads that become shorter than INT because of either quality or adapter trimming.", + "fa_icon": "fas fa-trash-alt" } }, "fa_icon": "fas fa-cut", @@ -409,6 +408,7 @@ "default": "", "properties": { "bamqc_regions_file": { + "type": "string", "format": "file-path", "exists": true, "mimetype": "text/plain", @@ -490,41 +490,6 @@ } } }, - "max_job_request_options": { - "title": "Max job request options", - "type": "object", - "fa_icon": "fab fa-acquisitions-incorporated", - "description": "Set the top limit for requested resources for any single job.", - "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.", - "properties": { - "max_cpus": { - "type": "integer", - "description": "Maximum number of CPUs that can be requested for any single job.", - "default": 16, - "fa_icon": "fas fa-microchip", - "hidden": true, - "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`" - }, - "max_memory": { - "type": "string", - "description": "Maximum amount of memory that can be requested for any single job.", - "default": "128.GB", - "fa_icon": "fas fa-memory", - "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$", - "hidden": true, - "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`" - }, - "max_time": { - "type": "string", - "description": "Maximum amount of time that can be requested for any single job.", - "default": "240.h", - "fa_icon": "far fa-clock", - "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$", - "hidden": true, - "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`" - } - } - }, "generic_options": { "title": "Generic options", "type": "object", @@ -532,12 +497,6 @@ "description": "Less common options for the pipeline, typically set in a config file.", "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", "properties": { - "help": { - "type": "boolean", - "description": "Display help text.", - "fa_icon": "fas fa-question-circle", - "hidden": true - }, "version": { "type": "boolean", "description": "Display version and exit.", @@ -613,69 +572,52 @@ "fa_icon": "fas fa-check-square", "hidden": true }, - "validationShowHiddenParams": { - "type": "boolean", - "fa_icon": "far fa-eye-slash", - "description": "Show all params when using `--help`", - "hidden": true, - "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." - }, - "validationFailUnrecognisedParams": { - "type": "boolean", - "fa_icon": "far fa-check-circle", - "description": "Validation of parameters fails when an unrecognised parameter is found.", - "hidden": true, - "help_text": "By default, when an unrecognised parameter is found, it returns a warinig." - }, - "validationLenientMode": { - "type": "boolean", + "pipelines_testdata_base_path": { + "type": "string", "fa_icon": "far fa-check-circle", - "description": "Validation of parameters in lenient more.", - "hidden": true, - "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)." + "description": "Base URL or local path to location of pipeline test dataset files", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/methylseq", + "hidden": true } } } }, "allOf": [ { - "$ref": "#/definitions/input_output_options" - }, - { - "$ref": "#/definitions/save_intermediate_files" + "$ref": "#/$defs/input_output_options" }, { - "$ref": "#/definitions/reference_genome_options" + "$ref": "#/$defs/save_intermediate_files" }, { - "$ref": "#/definitions/alignment_options" + "$ref": "#/$defs/reference_genome_options" }, { - "$ref": "#/definitions/special_library_types" + "$ref": "#/$defs/alignment_options" }, { - "$ref": "#/definitions/adapter_trimming" + "$ref": "#/$defs/special_library_types" }, { - "$ref": "#/definitions/bismark_options" + "$ref": "#/$defs/adapter_trimming" }, { - "$ref": "#/definitions/bwa_meth_options" + "$ref": "#/$defs/bismark_options" }, { - "$ref": "#/definitions/qualimap_options" + "$ref": "#/$defs/bwa_meth_options" }, { - "$ref": "#/definitions/skip_pipeline_steps" + "$ref": "#/$defs/qualimap_options" }, { - "$ref": "#/definitions/generic_options" + "$ref": "#/$defs/skip_pipeline_steps" }, { - "$ref": "#/definitions/max_job_request_options" + "$ref": "#/$defs/generic_options" }, { - "$ref": "#/definitions/institutional_config_options" + "$ref": "#/$defs/institutional_config_options" } ] } diff --git a/nf-test.config b/nf-test.config index 89243e51..b7a7023a 100644 --- a/nf-test.config +++ b/nf-test.config @@ -3,14 +3,20 @@ config { testsDir "." // nf-test directory including temporary files for each test - workDir "/tmp" - - // location of library folder that is added automatically to the classpath - libDir "tests/lib/" + workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" // location of an optional nextflow.config file specific for executing tests - configFile "nextflow.config" + configFile "tests/nextflow.config" // run all test with the defined docker profile from the main nextflow.config - profile "" + profile "test" + + // List of filenames or patterns that should be trigger a full test run + triggers 'nextflow.config', 'nf-test.config', 'conf/test.config', 'conf/test_full.config' + + // load the necessary plugins + plugins { + load "nft-bam@0.3.0" + load "nft-utils@0.0.3" + } } diff --git a/pyproject.toml b/pyproject.toml deleted file mode 100644 index 0d62beb6..00000000 --- a/pyproject.toml +++ /dev/null @@ -1,10 +0,0 @@ -# Config file for Python. Mostly used to configure linting of bin/check_samplesheet.py with Black. -# Should be kept the same as nf-core/tools to avoid fighting with template synchronisation. -[tool.black] -line-length = 120 -target_version = ["py37", "py38", "py39", "py310"] - -[tool.isort] -profile = "black" -known_first_party = ["nf_core"] -multi_line_output = 3 diff --git a/subworkflows/local/bismark.nf b/subworkflows/local/bismark.nf deleted file mode 100644 index 797da7a4..00000000 --- a/subworkflows/local/bismark.nf +++ /dev/null @@ -1,122 +0,0 @@ -/* - * bismark subworkflow - */ -include { BISMARK_ALIGN } from '../../modules/nf-core/bismark/align/main' -include { SAMTOOLS_SORT as SAMTOOLS_SORT_ALIGNED } from '../../modules/nf-core/samtools/sort/main' -include { SAMTOOLS_SORT as SAMTOOLS_SORT_DEDUPLICATED } from '../../modules/nf-core/samtools/sort/main' -include { BISMARK_DEDUPLICATE } from '../../modules/nf-core/bismark/deduplicate/main' -include { BISMARK_METHYLATIONEXTRACTOR } from '../../modules/nf-core/bismark/methylationextractor/main' -include { BISMARK_COVERAGE2CYTOSINE } from '../../modules/nf-core/bismark/coverage2cytosine/main' -include { BISMARK_REPORT } from '../../modules/nf-core/bismark/report/main' -include { BISMARK_SUMMARY } from '../../modules/nf-core/bismark/summary/main' - -workflow BISMARK { - take: - reads // channel: [ val(meta), [ reads ] ] - bismark_index // channel: /path/to/BismarkIndex/ - skip_deduplication // boolean: whether to deduplicate alignments - cytosine_report // boolean: whether the run coverage2cytosine - - main: - versions = Channel.empty() - - - /* - * Align with bismark - */ - BISMARK_ALIGN ( - reads, - bismark_index - ) - versions = versions.mix(BISMARK_ALIGN.out.versions) - - /* - * Sort raw output BAM - */ - SAMTOOLS_SORT_ALIGNED( - BISMARK_ALIGN.out.bam, - ) - versions = versions.mix(SAMTOOLS_SORT_ALIGNED.out.versions) - - if (skip_deduplication) { - alignments = BISMARK_ALIGN.out.bam - alignment_reports = BISMARK_ALIGN.out.report.map{ meta, report -> [ meta, report, [] ] } - } else { - /* - * Run deduplicate_bismark - */ - BISMARK_DEDUPLICATE( BISMARK_ALIGN.out.bam ) - - alignments = BISMARK_DEDUPLICATE.out.bam - alignment_reports = BISMARK_ALIGN.out.report.join(BISMARK_DEDUPLICATE.out.report) - versions = versions.mix(BISMARK_DEDUPLICATE.out.versions) - } - - /* - * Run bismark_methylation_extractor - */ - BISMARK_METHYLATIONEXTRACTOR ( - alignments, - bismark_index - ) - versions = versions.mix(BISMARK_METHYLATIONEXTRACTOR.out.versions) - - - /* - * Run coverage2cytosine - */ - if (cytosine_report) { - BISMARK_COVERAGE2CYTOSINE ( - BISMARK_METHYLATIONEXTRACTOR.out.coverage, - bismark_index - ) - versions = versions.mix(BISMARK_COVERAGE2CYTOSINE.out.versions) - } - - /* - * Generate bismark sample reports - */ - BISMARK_REPORT ( - alignment_reports - .join(BISMARK_METHYLATIONEXTRACTOR.out.report) - .join(BISMARK_METHYLATIONEXTRACTOR.out.mbias) - ) - versions = versions.mix(BISMARK_REPORT.out.versions) - - /* - * Generate bismark summary report - */ - BISMARK_SUMMARY ( - BISMARK_ALIGN.out.bam.collect{ it[1].name }.ifEmpty([]), - alignment_reports.collect{ it[1] }.ifEmpty([]), - alignment_reports.collect{ it[2] }.ifEmpty([]), - BISMARK_METHYLATIONEXTRACTOR.out.report.collect{ it[1] }.ifEmpty([]), - BISMARK_METHYLATIONEXTRACTOR.out.mbias.collect{ it[1] }.ifEmpty([]) - ) - versions = versions.mix(BISMARK_SUMMARY.out.versions) - - /* - * MODULE: Run samtools sort - */ - SAMTOOLS_SORT_DEDUPLICATED ( - alignments - ) - versions = versions.mix(SAMTOOLS_SORT_DEDUPLICATED.out.versions) - - /* - * Collect MultiQC inputs - */ - BISMARK_SUMMARY.out.summary.ifEmpty([]) - .mix(alignment_reports.collect{ it[1] }) - .mix(alignment_reports.collect{ it[2] }) - .mix(BISMARK_METHYLATIONEXTRACTOR.out.report.collect{ it[1] }) - .mix(BISMARK_METHYLATIONEXTRACTOR.out.mbias.collect{ it[1] }) - .mix(BISMARK_REPORT.out.report.collect{ it[1] }) - .set{ multiqc_files } - - emit: - bam = SAMTOOLS_SORT_ALIGNED.out.bam // channel: [ val(meta), [ bam ] ] ## sorted, non-deduplicated (raw) BAM from aligner - dedup = SAMTOOLS_SORT_DEDUPLICATED.out.bam // channel: [ val(meta), [ bam ] ] ## sorted, possibly deduplicated BAM - mqc = multiqc_files // path: *{html,txt} - versions // path: *.version.txt -} diff --git a/subworkflows/local/bismark/main.nf b/subworkflows/local/bismark/main.nf new file mode 100644 index 00000000..e94c0692 --- /dev/null +++ b/subworkflows/local/bismark/main.nf @@ -0,0 +1,159 @@ +/* + * Bismark subworkflow + */ +include { BISMARK_ALIGN } from '../../../modules/nf-core/bismark/align/main' +include { SAMTOOLS_SORT as SAMTOOLS_SORT_ALIGNED } from '../../../modules/nf-core/samtools/sort/main' +include { SAMTOOLS_SORT as SAMTOOLS_SORT_DEDUPLICATED } from '../../../modules/nf-core/samtools/sort/main' +include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_DEDUPLICATED } from '../../../modules/nf-core/samtools/index/main' +include { BISMARK_DEDUPLICATE } from '../../../modules/nf-core/bismark/deduplicate/main' +include { BISMARK_METHYLATIONEXTRACTOR } from '../../../modules/nf-core/bismark/methylationextractor/main' +include { BISMARK_COVERAGE2CYTOSINE } from '../../../modules/nf-core/bismark/coverage2cytosine/main' +include { BISMARK_REPORT } from '../../../modules/nf-core/bismark/report/main' +include { BISMARK_SUMMARY } from '../../../modules/nf-core/bismark/summary/main' + +workflow BISMARK { + take: + reads // channel: [ val(meta), [ reads ] ] + fasta // channel: /path/to/genome.fasta + bismark_index // channel: /path/to/BismarkIndex/ + skip_deduplication // boolean: whether to deduplicate alignments + cytosine_report // boolean: whether the run coverage2cytosine + + main: + + ch_versions = Channel.empty() + /* + * Align with bismark + */ + BISMARK_ALIGN ( + reads, + fasta, + bismark_index + ) + BISMARK_ALIGN.out.bam.dump(tag: 'BISMARK_ALIGN: bam') + BISMARK_ALIGN.out.report.dump(tag: 'BISMARK_ALIGN: report') + + ch_versions = ch_versions.mix(BISMARK_ALIGN.out.versions) + + /* + * Sort raw output BAM + */ + SAMTOOLS_SORT_ALIGNED( + BISMARK_ALIGN.out.bam, + [[:],[]] // Empty map and list as is optional input but required for nextflow + ) + SAMTOOLS_SORT_ALIGNED.out.bam.dump(tag: 'BISMARK/SAMTOOLS_SORT_ALIGNED: bam') + + ch_versions = ch_versions.mix(SAMTOOLS_SORT_ALIGNED.out.versions) + + if (skip_deduplication) { + alignments = BISMARK_ALIGN.out.bam + alignment_reports = BISMARK_ALIGN.out.report.map{ meta, report -> [ meta, report, [] ] } + + alignments.dump(tag: 'BISMARK/skip_deduplication: alignments') + alignment_reports.dump(tag: 'BISMARK/skip_deduplication: alignment_reports') + } else { + /* + * Run deduplicate_bismark + */ + BISMARK_DEDUPLICATE(BISMARK_ALIGN.out.bam) + + alignments = BISMARK_DEDUPLICATE.out.bam + alignment_reports = BISMARK_ALIGN.out.report.join(BISMARK_DEDUPLICATE.out.report) + ch_versions = ch_versions.mix(BISMARK_DEDUPLICATE.out.versions) + + alignments.dump(tag: 'BISMARK_DEDUPLICATE: alignments') + alignment_reports.dump(tag: 'BISMARK_DEDUPLICATE: alignment_reports') + } + + /* + * Run bismark_methylation_extractor + */ + BISMARK_METHYLATIONEXTRACTOR ( + alignments, + bismark_index + ) + BISMARK_METHYLATIONEXTRACTOR.out.report.dump(tag: 'BISMARK_METHYLATIONEXTRACTOR: report') + BISMARK_METHYLATIONEXTRACTOR.out.mbias.dump(tag: 'BISMARK_METHYLATIONEXTRACTOR: mbias') + + ch_versions = ch_versions.mix(BISMARK_METHYLATIONEXTRACTOR.out.versions) + + /* + * Run coverage2cytosine + */ + if (cytosine_report) { + BISMARK_COVERAGE2CYTOSINE ( + BISMARK_METHYLATIONEXTRACTOR.out.coverage, + fasta, + bismark_index + ) + BISMARK_COVERAGE2CYTOSINE.out.report.dump(tag: 'BISMARK_COVERAGE2CYTOSINE: report') + BISMARK_COVERAGE2CYTOSINE.out.coverage.dump(tag: 'BISMARK_COVERAGE2CYTOSINE: coverage') + BISMARK_COVERAGE2CYTOSINE.out.summary.dump(tag: 'BISMARK_COVERAGE2CYTOSINE: summary') + + ch_versions = ch_versions.mix(BISMARK_COVERAGE2CYTOSINE.out.versions) + } + + /* + * Generate bismark sample reports + */ + BISMARK_REPORT ( + alignment_reports + .join(BISMARK_METHYLATIONEXTRACTOR.out.report) + .join(BISMARK_METHYLATIONEXTRACTOR.out.mbias) + ) + BISMARK_REPORT.out.report.dump(tag: 'BISMARK_REPORT: report') + + ch_versions = ch_versions.mix(BISMARK_REPORT.out.versions) + + /* + * Generate bismark summary report + */ + BISMARK_SUMMARY ( + BISMARK_ALIGN.out.bam.collect{ it[1].name }.ifEmpty([]), + alignment_reports.collect{ it[1] }.ifEmpty([]), + alignment_reports.collect{ it[2] }.ifEmpty([]), + BISMARK_METHYLATIONEXTRACTOR.out.report.collect{ it[1] }.ifEmpty([]), + BISMARK_METHYLATIONEXTRACTOR.out.mbias.collect{ it[1] }.ifEmpty([]) + ) + BISMARK_SUMMARY.out.summary.dump(tag: 'BISMARK_REPORT: summary') + + ch_versions = ch_versions.mix(BISMARK_SUMMARY.out.versions) + + /* + * MODULE: Run samtools sort + */ + SAMTOOLS_SORT_DEDUPLICATED ( + alignments, + [[:],[]] // Empty map and list as is optional input but required for nextflow + ) + SAMTOOLS_SORT_DEDUPLICATED.out.bam.dump(tag: 'BISMARK/SAMTOOLS_SORT_DEDUPLICATED: bam') + + ch_versions = ch_versions.mix(SAMTOOLS_SORT_DEDUPLICATED.out.versions) + + /* + * MODULE: Run samtools index on dedup bam + */ + SAMTOOLS_INDEX_DEDUPLICATED(SAMTOOLS_SORT_DEDUPLICATED.out.bam) + + SAMTOOLS_INDEX_DEDUPLICATED.out.bai.dump(tag: 'BISMARK/SAMTOOLS_INDEX_DEDUPLICATED: bai') + + ch_versions = ch_versions.mix(SAMTOOLS_INDEX_DEDUPLICATED.out.versions) + + /* + * Collect MultiQC inputs + */ + BISMARK_SUMMARY.out.summary.ifEmpty([]) + .mix(alignment_reports.collect{ it[1] }) + .mix(alignment_reports.collect{ it[2] }) + .mix(BISMARK_METHYLATIONEXTRACTOR.out.report.collect{ it[1] }) + .mix(BISMARK_METHYLATIONEXTRACTOR.out.mbias.collect{ it[1] }) + .mix(BISMARK_REPORT.out.report.collect{ it[1] }) + .set{ multiqc_files } + + emit: + bam = SAMTOOLS_SORT_ALIGNED.out.bam // channel: [ val(meta), [ bam ] ] ## sorted, non-deduplicated (raw) BAM from aligner + dedup = SAMTOOLS_SORT_DEDUPLICATED.out.bam // channel: [ val(meta), [ bam ] ] ## sorted, possibly deduplicated BAM + mqc = multiqc_files // path: *{html,txt} + versions = ch_versions // path: *.version.txt +} diff --git a/subworkflows/local/bismark/nextflow.config b/subworkflows/local/bismark/nextflow.config new file mode 100644 index 00000000..d58d65ad --- /dev/null +++ b/subworkflows/local/bismark/nextflow.config @@ -0,0 +1,32 @@ + +includeConfig "../../../modules/nf-core/bismark/align/nextflow.config" +includeConfig "../../../modules/nf-core/samtools/sort/nextflow.config" +includeConfig "../../../modules/nf-core/bismark/deduplicate/nextflow.config" +includeConfig "../../../modules/nf-core/bismark/methylationextractor/nextflow.config" +includeConfig "../../../modules/nf-core/bismark/coverage2cytosine/nextflow.config" +includeConfig "../../../modules/nf-core/bismark/report/nextflow.config" +includeConfig "../../../modules/nf-core/bismark/summary/nextflow.config" + +process { + withName: SAMTOOLS_SORT_DEDUPLICATED { + ext.prefix = { "${meta.id}.deduplicated.sorted" } + publishDir = [ + [ + path: { "${params.outdir}/${params.aligner}/deduplicated/" }, + mode: params.publish_dir_mode, + pattern: "*.deduplicated.sorted.bam" + ] + ] + } + + withName: SAMTOOLS_INDEX_DEDUPLICATED { + ext.args = "" + publishDir = [ + [ + path: { "${params.outdir}/${params.aligner}/deduplicated/" }, + mode: params.publish_dir_mode, + pattern: "*.bai" + ] + ] + } +} diff --git a/subworkflows/local/bismark/tests/bismark_hisat.nf.test b/subworkflows/local/bismark/tests/bismark_hisat.nf.test new file mode 100644 index 00000000..1f1070b3 --- /dev/null +++ b/subworkflows/local/bismark/tests/bismark_hisat.nf.test @@ -0,0 +1,70 @@ +nextflow_workflow { + + name "Test Workflow BISMARK_HISAT" + script "../main.nf" + workflow "BISMARK" + config "../nextflow.config" + + setup { + run("UNTAR") { + script "../../../../modules/nf-core/untar/main.nf" + process { + """ + input[0] = [ + [:], + file(params.pipelines_testdata_base_path + 'reference/Hisat2_Index.tar.gz', checkIfExists: true) + ] + """ + } + } + } + + test("Bismark_Hisat | save_reference") { + + when { + params { + aligner = "bismark_hisat" + publish_dir_mode = 'copy' + unmapped = false + save_align_intermeds = false + skip_deduplication = false + cytosine_report = false + rrbs = false + nomeseq = false + slamseq = false + save_reference = true + outdir = "results" + } + workflow { + """ + + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file(params.pipelines_testdata_base_path + 'testdata/SRR389222_sub1.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ + [:], + file(params.pipelines_testdata_base_path + 'reference/genome.fa', checkIfExists: true) + ]) + input[2] = UNTAR.out.untar + input[3] = params.skip_deduplication + input[4] = params.cytosine_report + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.bam.collect { bam(it[1]).getReadsMD5() }, + workflow.out.dedup.collect { bam(it[1]).getReadsMD5() }, + //workflow.out.mqc, + workflow.out.versions + ).match() } + ) + } + + } + +} diff --git a/subworkflows/local/bismark/tests/bismark_hisat.nf.test.snap b/subworkflows/local/bismark/tests/bismark_hisat.nf.test.snap new file mode 100644 index 00000000..a531a2e7 --- /dev/null +++ b/subworkflows/local/bismark/tests/bismark_hisat.nf.test.snap @@ -0,0 +1,27 @@ +{ + "Bismark_Hisat | save_reference": { + "content": [ + [ + "3a6485d719fcaf868c7f95c8f10a3f3c" + ], + [ + "dae445da532c973dc9149f3ceba2d2c5" + ], + [ + "versions.yml:md5,2273d537ccb64f2260adeb6844523d73", + "versions.yml:md5,6a04613f312dd68246d992a7f6fa03a5", + "versions.yml:md5,c06f3e25000330e948f7a35708270f3f", + "versions.yml:md5,c2ad6c469b4d15c963f03b2228376a80", + "versions.yml:md5,cb4a7015750ef1e0e504c56acb72a799", + "versions.yml:md5,cb8dda62996be2045f2ad33831c6b74c", + "versions.yml:md5,cd3f634936e8c40265e766e5f5d07f15", + "versions.yml:md5,cfb4c81c53e84715cbf50b702a84e457" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-20T11:17:46.351442694" + } +} diff --git a/subworkflows/local/bismark/tests/main.nf.test b/subworkflows/local/bismark/tests/main.nf.test new file mode 100644 index 00000000..b38cbdbc --- /dev/null +++ b/subworkflows/local/bismark/tests/main.nf.test @@ -0,0 +1,70 @@ +nextflow_workflow { + + name "Test Workflow BISMARK" + script "../main.nf" + workflow "BISMARK" + config "../nextflow.config" + + setup { + run("UNTAR") { + script "../../../../modules/nf-core/untar/main.nf" + process { + """ + input[0] = [ + [:], + file(params.pipelines_testdata_base_path + 'reference/Bowtie2_Index.tar.gz', checkIfExists: true) + ] + """ + } + } + } + + test("Bismark | save_reference") { + + when { + params { + aligner = "bismark" + publish_dir_mode = 'copy' + unmapped = false + save_align_intermeds = false + skip_deduplication = false + cytosine_report = false + rrbs = false + nomeseq = false + slamseq = false + save_reference = true + outdir = "results" + } + workflow { + """ + + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file(params.pipelines_testdata_base_path + 'testdata/SRR389222_sub1.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ + [:], + file(params.pipelines_testdata_base_path + 'reference/genome.fa', checkIfExists: true) + ]) + input[2] = UNTAR.out.untar + input[3] = params.skip_deduplication + input[4] = params.cytosine_report + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.bam.collect { bam(it[1]).getReadsMD5() }, + workflow.out.dedup.collect { bam(it[1]).getReadsMD5() }, + //workflow.out.mqc, + workflow.out.versions + ).match() } + ) + } + + } + +} diff --git a/subworkflows/local/bismark/tests/main.nf.test.snap b/subworkflows/local/bismark/tests/main.nf.test.snap new file mode 100644 index 00000000..6757ea79 --- /dev/null +++ b/subworkflows/local/bismark/tests/main.nf.test.snap @@ -0,0 +1,27 @@ +{ + "Bismark | save_reference": { + "content": [ + [ + "d6951f6d3381e22becf62553a37c0f3f" + ], + [ + "35d55bee1ca653931716e40dac4aba30" + ], + [ + "versions.yml:md5,2273d537ccb64f2260adeb6844523d73", + "versions.yml:md5,6a04613f312dd68246d992a7f6fa03a5", + "versions.yml:md5,c06f3e25000330e948f7a35708270f3f", + "versions.yml:md5,c2ad6c469b4d15c963f03b2228376a80", + "versions.yml:md5,cb4a7015750ef1e0e504c56acb72a799", + "versions.yml:md5,cb8dda62996be2045f2ad33831c6b74c", + "versions.yml:md5,cd3f634936e8c40265e766e5f5d07f15", + "versions.yml:md5,cfb4c81c53e84715cbf50b702a84e457" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-20T11:14:29.732866935" + } +} diff --git a/subworkflows/local/bwameth.nf b/subworkflows/local/bwameth.nf deleted file mode 100644 index 5004d8b9..00000000 --- a/subworkflows/local/bwameth.nf +++ /dev/null @@ -1,113 +0,0 @@ -/* - * bwameth subworkflow - */ -include { SAMTOOLS_STATS } from '../../modules/nf-core/samtools/stats/main' -include { SAMTOOLS_FLAGSTAT } from '../../modules/nf-core/samtools/flagstat/main' -include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_ALIGNMENTS } from '../../modules/nf-core/samtools/index/main' -include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_DEDUPLICATED } from '../../modules/nf-core/samtools/index/main' -include { SAMTOOLS_SORT } from '../../modules/nf-core/samtools/sort/main' -include { PICARD_MARKDUPLICATES } from '../../modules/nf-core/picard/markduplicates/main' -include { BWAMETH_ALIGN } from '../../modules/nf-core/bwameth/align/main' -include { METHYLDACKEL_EXTRACT } from '../../modules/nf-core/methyldackel/extract/main' -include { METHYLDACKEL_MBIAS } from '../../modules/nf-core/methyldackel/mbias/main' - -workflow BWAMETH { - take: - reads // channel: [ val(meta), [ reads ] ] - bwameth_index // channel: /path/to/bwa_index/ - fasta // channel: /path/to/genome.fa - fasta_index // channel: /path/to/genome.fa.fai - skip_deduplication // boolean: whether to deduplicate alignments - - main: - versions = Channel.empty() - - /* - * Align with bwameth - */ - BWAMETH_ALIGN ( - reads, - bwameth_index - ) - versions = versions.mix(BWAMETH_ALIGN.out.versions) - - /* - * Sort raw output BAM - */ - SAMTOOLS_SORT (BWAMETH_ALIGN.out.bam) - versions = versions.mix(SAMTOOLS_SORT.out.versions) - - /* - * Run samtools index on alignment - */ - SAMTOOLS_INDEX_ALIGNMENTS (SAMTOOLS_SORT.out.bam) - versions = versions.mix(SAMTOOLS_INDEX_ALIGNMENTS.out.versions) - - /* - * Run samtools flagstat and samtools stats - */ - SAMTOOLS_FLAGSTAT( BWAMETH_ALIGN.out.bam.join(SAMTOOLS_INDEX_ALIGNMENTS.out.bai) ) - SAMTOOLS_STATS( BWAMETH_ALIGN.out.bam.join(SAMTOOLS_INDEX_ALIGNMENTS.out.bai), [] ) - versions = versions.mix(SAMTOOLS_FLAGSTAT.out.versions) - versions = versions.mix(SAMTOOLS_STATS.out.versions) - - if (skip_deduplication) { - alignments = SAMTOOLS_SORT.out.bam - bam_index = SAMTOOLS_INDEX_ALIGNMENTS.out.bai - picard_metrics = Channel.empty() - picard_version = Channel.empty() - } else { - /* - * Run Picard MarkDuplicates - */ - PICARD_MARKDUPLICATES ( - SAMTOOLS_SORT.out.bam, - fasta, - fasta_index - ) - /* - * Run samtools index on deduplicated alignment - */ - SAMTOOLS_INDEX_DEDUPLICATED (PICARD_MARKDUPLICATES.out.bam) - - alignments = PICARD_MARKDUPLICATES.out.bam - bam_index = SAMTOOLS_INDEX_DEDUPLICATED.out.bai - picard_metrics = PICARD_MARKDUPLICATES.out.metrics - picard_version = PICARD_MARKDUPLICATES.out.versions - versions = versions.mix(PICARD_MARKDUPLICATES.out.versions) - } - - - /* - * Extract per-base methylation and plot methylation bias - */ - - METHYLDACKEL_EXTRACT( - alignments.join(bam_index), - fasta, - fasta_index - ) - METHYLDACKEL_MBIAS( - alignments.join(bam_index), - fasta, - fasta_index - ) - versions = versions.mix(METHYLDACKEL_EXTRACT.out.versions) - versions = versions.mix(METHYLDACKEL_MBIAS.out.versions) - - /* - * Collect MultiQC inputs - */ - picard_metrics.collect{ it[1] } - .mix(SAMTOOLS_FLAGSTAT.out.flagstat.collect{ it[1] }) - .mix(SAMTOOLS_STATS.out.stats.collect{ it[1] }) - .mix(METHYLDACKEL_EXTRACT.out.bedgraph.collect{ it[1] }) - .mix(METHYLDACKEL_MBIAS.out.txt.collect{ it[1] }) - .set{ multiqc_files } - - emit: - bam = SAMTOOLS_SORT.out.bam // channel: [ val(meta), [ bam ] ] ## sorted, non-deduplicated (raw) BAM from aligner - dedup = alignments // channel: [ val(meta), [ bam ] ] ## sorted, possibly deduplicated BAM - mqc = multiqc_files // path: *{html,txt} - versions // path: *.version.txt -} diff --git a/subworkflows/local/bwameth/main.nf b/subworkflows/local/bwameth/main.nf new file mode 100644 index 00000000..11c60eae --- /dev/null +++ b/subworkflows/local/bwameth/main.nf @@ -0,0 +1,136 @@ +/* + * bwameth subworkflow + */ +include { BWAMETH_ALIGN } from '../../../modules/nf-core/bwameth/align/main' +include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main' +include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_ALIGNMENTS } from '../../../modules/nf-core/samtools/index/main' +include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/main' +include { SAMTOOLS_STATS } from '../../../modules/nf-core/samtools/stats/main' +include { PICARD_MARKDUPLICATES } from '../../../modules/nf-core/picard/markduplicates/main' +include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_DEDUPLICATED } from '../../../modules/nf-core/samtools/index/main' +include { METHYLDACKEL_EXTRACT } from '../../../modules/nf-core/methyldackel/extract/main' +include { METHYLDACKEL_MBIAS } from '../../../modules/nf-core/methyldackel/mbias/main' + +workflow BWAMETH { + take: + reads // channel: [ val(meta), [ reads ] ] + bwameth_index // channel: /path/to/bwa_index/ + fasta // channel: /path/to/genome.fa + fasta_index // channel: /path/to/genome.fa.fai + skip_deduplication // boolean: whether to deduplicate alignments + + main: + ch_versions = Channel.empty() + + /* + * Align with bwameth + */ + BWAMETH_ALIGN ( + reads, + fasta, + bwameth_index + ) + BWAMETH_ALIGN.out.bam.dump(tag: 'BWAMETH_ALIGN: bam') + + ch_versions = ch_versions.mix(BWAMETH_ALIGN.out.versions) + + /* + * Sort raw output BAM + */ + SAMTOOLS_SORT ( + BWAMETH_ALIGN.out.bam, + [[:],[]] // Empty map and list as is optional input but required for nextflow + ) + SAMTOOLS_SORT.out.bam.dump(tag: 'BWAMETH/SAMTOOLS_SORT: bam') + + ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions) + + /* + * Run samtools index on alignment + */ + SAMTOOLS_INDEX_ALIGNMENTS (SAMTOOLS_SORT.out.bam) + SAMTOOLS_INDEX_ALIGNMENTS.out.bai.dump(tag: 'BWAMETH/SAMTOOLS_INDEX_ALIGNMENTS: bai') + + ch_versions = ch_versions.mix(SAMTOOLS_INDEX_ALIGNMENTS.out.versions) + + /* + * Run samtools flagstat and samtools stats + */ + SAMTOOLS_FLAGSTAT(BWAMETH_ALIGN.out.bam.join(SAMTOOLS_INDEX_ALIGNMENTS.out.bai)) + SAMTOOLS_FLAGSTAT.out.flagstat.dump(tag: 'BWAMETH/SAMTOOLS_FLAGSTAT: flagstat') + + SAMTOOLS_STATS( + BWAMETH_ALIGN.out.bam.join(SAMTOOLS_INDEX_ALIGNMENTS.out.bai), + [[:],[]] + ) + SAMTOOLS_STATS.out.stats.dump(tag: 'BWAMETH/SAMTOOLS_STATS: flagstat') + + ch_versions = ch_versions.mix(SAMTOOLS_FLAGSTAT.out.versions) + ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions) + + if (skip_deduplication) { + alignments = SAMTOOLS_SORT.out.bam + bam_index = SAMTOOLS_INDEX_ALIGNMENTS.out.bai + picard_metrics = Channel.empty() + picard_version = Channel.empty() + } else { + /* + * Run Picard MarkDuplicates + */ + PICARD_MARKDUPLICATES ( + SAMTOOLS_SORT.out.bam, + fasta, + fasta_index.map{ fasta_index -> [[:], fasta_index]}, + ) + PICARD_MARKDUPLICATES.out.bam.dump(tag: 'BWAMETH/PICARD_MARKDUPLICATES: bam') + /* + * Run samtools index on deduplicated alignment + */ + SAMTOOLS_INDEX_DEDUPLICATED (PICARD_MARKDUPLICATES.out.bam) + + alignments = PICARD_MARKDUPLICATES.out.bam + bam_index = SAMTOOLS_INDEX_DEDUPLICATED.out.bai + picard_metrics = PICARD_MARKDUPLICATES.out.metrics + picard_version = PICARD_MARKDUPLICATES.out.versions + ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES.out.versions) + } + + + /* + * Extract per-base methylation and plot methylation bias + */ + + METHYLDACKEL_EXTRACT( + alignments.join(bam_index), + fasta.map{ meta, fasta_file -> [fasta_file]}, + fasta_index + ) + METHYLDACKEL_EXTRACT.out.bedgraph.dump(tag: 'BWAMETH/METHYLDACKEL_EXTRACT: bedgraph') + METHYLDACKEL_EXTRACT.out.methylkit.dump(tag: 'BWAMETH/METHYLDACKEL_EXTRACT: methylkit') + + METHYLDACKEL_MBIAS( + alignments.join(bam_index), + fasta.map{ meta, fasta_file -> [fasta_file]}, + fasta_index + ) + METHYLDACKEL_MBIAS.out.txt.dump(tag: 'BWAMETH/METHYLDACKEL_MBIAS: txt') + + ch_versions = ch_versions.mix(METHYLDACKEL_EXTRACT.out.versions) + ch_versions = ch_versions.mix(METHYLDACKEL_MBIAS.out.versions) + + /* + * Collect MultiQC inputs + */ + picard_metrics.collect{ it[1] } + .mix(SAMTOOLS_FLAGSTAT.out.flagstat.collect{ it[1] }) + .mix(SAMTOOLS_STATS.out.stats.collect{ it[1] }) + .mix(METHYLDACKEL_EXTRACT.out.bedgraph.collect{ it[1] }) + .mix(METHYLDACKEL_MBIAS.out.txt.collect{ it[1] }) + .set{ multiqc_files } + + emit: + bam = SAMTOOLS_SORT.out.bam // channel: [ val(meta), [ bam ] ] ## sorted, non-deduplicated (raw) BAM from aligner + dedup = alignments // channel: [ val(meta), [ bam ] ] ## sorted, possibly deduplicated BAM + mqc = multiqc_files // path: *{html,txt} + versions = ch_versions // path: *.version.txt +} diff --git a/subworkflows/local/bwameth/nextflow.config b/subworkflows/local/bwameth/nextflow.config new file mode 100644 index 00000000..4eff78d7 --- /dev/null +++ b/subworkflows/local/bwameth/nextflow.config @@ -0,0 +1,36 @@ + +includeConfig "../../../modules/nf-core/bwameth/align/nextflow.config" +includeConfig "../../../modules/nf-core/samtools/sort/nextflow.config" + +includeConfig "../../../modules/nf-core/samtools/flagstat/nextflow.config" +includeConfig "../../../modules/nf-core/samtools/stats/nextflow.config" +includeConfig "../../../modules/nf-core/picard/markduplicates/nextflow.config" +includeConfig "../../../modules/nf-core/methyldackel/extract/nextflow.config" +includeConfig "../../../modules/nf-core/methyldackel/mbias/nextflow.config" + +process { + + withName: SAMTOOLS_INDEX_ALIGNMENTS { + ext.args = "" + publishDir = [ + [ + path: { "${params.outdir}/${params.aligner}/alignments/" }, + mode: params.publish_dir_mode, + pattern: "*.bam.bai", + enabled: params.save_align_intermeds + ] + ] + } + + withName: SAMTOOLS_INDEX_DEDUPLICATED { + ext.args = "" + publishDir = [ + [ + path: { "${params.outdir}/${params.aligner}/deduplicated/" }, + mode: params.publish_dir_mode, + pattern: "*.bam.bai" + ] + ] + } + +} diff --git a/subworkflows/local/bwameth/tests/main.nf.test b/subworkflows/local/bwameth/tests/main.nf.test new file mode 100644 index 00000000..21aadf8a --- /dev/null +++ b/subworkflows/local/bwameth/tests/main.nf.test @@ -0,0 +1,68 @@ +nextflow_workflow { + + name "Test Workflow BWAMETH" + script "../main.nf" + workflow "BWAMETH" + config "../nextflow.config" + + setup { + run("UNTAR") { + script "../../../../modules/nf-core/untar/main.nf" + process { + """ + input[0] = [ + [:], + file(params.pipelines_testdata_base_path + 'reference/Bwameth_Index.tar.gz', checkIfExists: true) + ] + """ + } + } + } + + test("Bwameth | save_reference") { + + when { + params { + aligner = "bwameth" + publish_dir_mode = 'copy' + outdir = "results" + save_reference = true + save_align_intermeds = false + min_depth = 0 + comprehensive = false + ignore_flags = false + methyl_kit = false + skip_deduplication = false + } + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file(params.pipelines_testdata_base_path + 'testdata/SRR389222_sub1.fastq.gz', checkIfExists: true) + ]) + input[1] = UNTAR.out.untar + input[2] = Channel.of([ + [:], + file(params.pipelines_testdata_base_path + 'reference/genome.fa', checkIfExists: true) + ]) + input[3] = Channel.of(file(params.pipelines_testdata_base_path + 'reference/genome.fa.fai', checkIfExists: true)) + input[4] = params.skip_deduplication + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.bam.collect { bam(it[1]).getReadsMD5() }, + workflow.out.dedup.collect { bam(it[1]).getReadsMD5() }, + //workflow.out.mqc, + workflow.out.versions + ).match() } + ) + } + + } + +} diff --git a/subworkflows/local/bwameth/tests/main.nf.test.snap b/subworkflows/local/bwameth/tests/main.nf.test.snap new file mode 100644 index 00000000..3834e919 --- /dev/null +++ b/subworkflows/local/bwameth/tests/main.nf.test.snap @@ -0,0 +1,27 @@ +{ + "Bwameth | save_reference": { + "content": [ + [ + "37ec1c6338cc3fee7ab1cb2d48dba38" + ], + [ + "37ec1c6338cc3fee7ab1cb2d48dba38" + ], + [ + "versions.yml:md5,0906211fa5d0f6fd287c24407a882ae6", + "versions.yml:md5,204d3bc1f6fff3c1f7ea1f014f256fd7", + "versions.yml:md5,2b54b53cdedbbd547bc6bc3623dcc622", + "versions.yml:md5,38a8061118fdcb6215a31e60419df107", + "versions.yml:md5,5e8c932b160898dbcf29469f4ea6c978", + "versions.yml:md5,88592f164662fc6e5389899dbf472f53", + "versions.yml:md5,b935a799534fa7094fe81a723df04ecf", + "versions.yml:md5,c3658cdda0f57c6d7f0c57e820921eb4" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-21T18:23:18.006459111" + } +} \ No newline at end of file diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf deleted file mode 100644 index 877541ea..00000000 --- a/subworkflows/local/prepare_genome.nf +++ /dev/null @@ -1,80 +0,0 @@ -// -// Prepare reference genome files -// - -include { UNTAR } from '../../modules/nf-core/untar/main' -include { BISMARK_GENOMEPREPARATION } from '../../modules/nf-core/bismark/genomepreparation/main' -include { BWAMETH_INDEX } from '../../modules/nf-core/bwameth/index/main' -include { SAMTOOLS_FAIDX } from '../../modules/nf-core/samtools/faidx/main' - -workflow PREPARE_GENOME { - - main: - ch_versions = Channel.empty() - ch_fasta = Channel.empty() - ch_bismark_index = Channel.empty() - ch_bwameth_index = Channel.empty() - ch_fasta_index = Channel.empty() - - // FASTA, if supplied - if (params.fasta) { - ch_fasta = Channel.value(file(params.fasta)) - } - - // Aligner: bismark or bismark_hisat - if( params.aligner =~ /bismark/ ){ - - /* - * Generate bismark index if not supplied - */ - if (params.bismark_index) { - if (params.bismark_index.endsWith('.gz')) { - ch_bismark_index = UNTAR ( [ [:], file(params.bismark_index) ] ).untar.map { it[1] } - } else { - ch_bismark_index = Channel.value(file(params.bismark_index)) - } - } else { - BISMARK_GENOMEPREPARATION(ch_fasta) - ch_bismark_index = BISMARK_GENOMEPREPARATION.out.index - ch_versions = ch_versions.mix(BISMARK_GENOMEPREPARATION.out.versions) - } - - } - // Aligner: bwameth - else if ( params.aligner == 'bwameth' ){ - - /* - * Generate bwameth index if not supplied - */ - if (params.bwa_meth_index) { - if (params.bwa_meth_index.endsWith('.tar.gz')) { - ch_bismark_index = UNTAR ( [ [:], file(params.bwa_meth_index) ] ).untar.map { it[1] } - } else { - ch_bismark_index = Channel.value(file(params.bwa_meth_index)) - } - } else { - BWAMETH_INDEX(ch_fasta) - ch_bwameth_index = BWAMETH_INDEX.out.index - ch_versions = ch_versions.mix(BWAMETH_INDEX.out.versions) - } - - /* - * Generate fasta index if not supplied - */ - if (params.fasta_index) { - ch_fasta_index = Channel.value(file(params.fasta_index)) - } else { - SAMTOOLS_FAIDX([[:], ch_fasta]) - ch_fasta_index = SAMTOOLS_FAIDX.out.fai.map{ return(it[1])} - ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions) - } - } - - emit: - fasta = ch_fasta // channel: path(genome.fasta) - bismark_index = ch_bismark_index // channel: path(genome.fasta) - bwameth_index = ch_bwameth_index // channel: path(genome.fasta) - fasta_index = ch_fasta_index // channel: path(genome.fasta) - versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ] - -} diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf new file mode 100644 index 00000000..8f8523a1 --- /dev/null +++ b/subworkflows/local/prepare_genome/main.nf @@ -0,0 +1,108 @@ +// +// Prepare reference genome files +// + +include { UNTAR } from '../../../modules/nf-core/untar/main' +include { GUNZIP } from '../../../modules/nf-core/gunzip/main' +include { BISMARK_GENOMEPREPARATION } from '../../../modules/nf-core/bismark/genomepreparation/main' +include { BWAMETH_INDEX } from '../../../modules/nf-core/bwameth/index/main' +include { SAMTOOLS_FAIDX } from '../../../modules/nf-core/samtools/faidx/main' + +workflow PREPARE_GENOME { + take: + fasta // file: /path/to/genome.fasta + fasta_index // file: /path/to/genome.fasta.fai + bismark_index // directory: /path/to/bismark/index/ + bwameth_index // directory: /path/to/bwameth/index/ + + main: + ch_versions = Channel.empty() + ch_fasta = Channel.empty() + ch_fasta_index = Channel.empty() + ch_bismark_index = Channel.empty() + ch_bwameth_index = Channel.empty() + + // FASTA, if supplied + if (fasta.endsWith('.gz')) { + ch_fasta = GUNZIP ([ [:], file(fasta, checkIfExists: true) ]).gunzip.map { it[1] } + ch_versions = ch_versions.mix(GUNZIP.out.versions) + } else { + ch_fasta = Channel.value([[:], file(fasta, checkIfExists: true)]) + } + ch_fasta.dump(tag: 'PREPARE_GENOME: ch_fasta') + + // Aligner: bismark or bismark_hisat + if( params.aligner =~ /bismark/ ){ + /* + * Generate bismark index if not supplied + */ + if (bismark_index) { + if (bismark_index.endsWith('.gz')) { + ch_bismark_index = UNTAR ([ [:], file(bismark_index) ]).untar + ch_bismark_index.dump(tag: 'PREPARE_GENOME/UNTAR: ch_bismark_index') + + ch_versions = ch_versions.mix(UNTAR.out.versions) + } else { + ch_bismark_index = Channel.value([[:], file(bismark_index, checkIfExists: true)]) + ch_bismark_index.dump(tag: 'PREPARE_GENOME: ch_bismark_index') + } + } else { + BISMARK_GENOMEPREPARATION(ch_fasta) + + ch_bismark_index = BISMARK_GENOMEPREPARATION.out.index + ch_bismark_index.dump(tag: 'PREPARE_GENOME: ch_bismark_index') + + ch_versions = ch_versions.mix(BISMARK_GENOMEPREPARATION.out.versions) + } + + } + // Aligner: bwameth + else if ( params.aligner == 'bwameth' ){ + /* + * Generate bwameth index if not supplied + */ + if (bwameth_index) { + if (bwameth_index.endsWith('.tar.gz')) { + ch_bwameth_index = UNTAR ([ [:], file(bwameth_index, checkIfExists: true) ]).untar + ch_bwameth_index.dump(tag: 'PREPARE_GENOME/UNTAR: ch_bwameth_index') + + ch_versions = ch_versions.mix(UNTAR.out.versions) + } else { + ch_bwameth_index = Channel.value([[:], file(bwameth_index, checkIfExists: true)]) + ch_bwameth_index.dump(tag: 'PREPARE_GENOME: ch_bwameth_index') + } + } else { + BWAMETH_INDEX(ch_fasta) + + ch_bwameth_index = BWAMETH_INDEX.out.index + ch_bwameth_index.dump(tag: 'PREPARE_GENOME: ch_bwameth_index') + + ch_versions = ch_versions.mix(BWAMETH_INDEX.out.versions) + } + + /* + * Generate fasta index if not supplied + */ + if (fasta_index) { + ch_fasta_index = Channel.value(file(fasta_index, checkIfExists: true)) + ch_fasta_index.dump(tag: 'PREPARE_GENOME: ch_fasta_index') + } else { + SAMTOOLS_FAIDX( + ch_fasta, + [[:], []] + ) + ch_fasta_index = SAMTOOLS_FAIDX.out.fai.map{ return(it[1])} + ch_fasta_index.dump(tag: 'PREPARE_GENOME: ch_fasta_index') + + ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions) + } + } + + emit: + fasta = ch_fasta // channel: path(genome.fasta) + bismark_index = ch_bismark_index // channel: path(genome.fasta) + bwameth_index = ch_bwameth_index // channel: path(genome.fasta) + fasta_index = ch_fasta_index // channel: path(genome.fasta) + versions = ch_versions // channel: [ versions.yml ] + +} diff --git a/subworkflows/local/prepare_genome/nextflow.config b/subworkflows/local/prepare_genome/nextflow.config new file mode 100644 index 00000000..39f3f167 --- /dev/null +++ b/subworkflows/local/prepare_genome/nextflow.config @@ -0,0 +1,4 @@ + +includeConfig "../../../modules/nf-core/bismark/genomepreparation/nextflow.config" +includeConfig "../../../modules/nf-core/samtools/faidx/nextflow.config" +includeConfig "../../../modules/nf-core/bwameth/index/nextflow.config" diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test b/subworkflows/local/prepare_genome/tests/main.nf.test new file mode 100644 index 00000000..c7f20b6a --- /dev/null +++ b/subworkflows/local/prepare_genome/tests/main.nf.test @@ -0,0 +1,105 @@ +nextflow_workflow { + + name "Test Workflow PREPARE_GENOME" + script "../main.nf" + workflow "PREPARE_GENOME" + config "../nextflow.config" + + test("Generate Bismark Index (bowtie2)") { + + when { + params { + aligner = "bismark" + publish_dir_mode = copy + save_reference = false + slamseq = false + } + workflow { + """ + input[0] = file(params.pipelines_testdata_base_path + 'reference/genome.fa', checkIfExists: true) // fasta + input[1] = [] // fasta_index + input[2] = [] // bismark_index + input[3] = [] // bwameth_index + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.fasta, + workflow.out.bismark_index, + workflow.out.versions + ).match() } + ) + } + + } + + test("Generate Bismark Index (hisat2)") { + + when { + params { + aligner = "bismark_hisat" + publish_dir_mode = copy + save_reference = false + slamseq = false + } + workflow { + """ + input[0] = file(params.pipelines_testdata_base_path + 'reference/genome.fa', checkIfExists: true) // fasta + input[1] = [] // fasta_index + input[2] = [] // bismark_index + input[3] = [] // bwameth_index + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.fasta, + workflow.out.bismark_index, + workflow.out.versions + ).match() } + ) + } + + } + + test("Generate Bwameth Index") { + + when { + params { + aligner = "bwameth" + publish_dir_mode = copy + save_reference = false + slamseq = false + } + workflow { + """ + input[0] = file(params.pipelines_testdata_base_path + 'reference/genome.fa', checkIfExists: true) // fasta + input[1] = [] // fasta_index + input[2] = [] // bismark_index + input[3] = [] // bwameth_index + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.fasta, + workflow.out.fasta_index, + workflow.out.bwameth_index, + workflow.out.versions + ).match() } + ) + } + + } + +} diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test.snap b/subworkflows/local/prepare_genome/tests/main.nf.test.snap new file mode 100644 index 00000000..73d4db88 --- /dev/null +++ b/subworkflows/local/prepare_genome/tests/main.nf.test.snap @@ -0,0 +1,143 @@ +{ + "Generate Bismark Index (hisat2)": { + "content": [ + [ + [ + { + + }, + "/nf-core/test-datasets/raw/methylseq/reference/genome.fa" + ] + ], + [ + [ + { + + }, + [ + [ + [ + "BS_CT.1.ht2:md5,273c7686fc1dc7d93e36433592367f81", + "BS_CT.2.ht2:md5,752a03fc364115fc910e5a28ae154382", + "BS_CT.3.ht2:md5,b41e72eefad74e8ede411c78a5bd5dee", + "BS_CT.4.ht2:md5,02b3d1855a67fd9cbb4c411406a22fde", + "BS_CT.5.ht2:md5,d117de4c2c910a1ae7f0459c11ba6018", + "BS_CT.6.ht2:md5,4097a785a8d1ca92489d83b4c613a50b", + "BS_CT.7.ht2:md5,9013eccd91ad614d7893c739275a394f", + "BS_CT.8.ht2:md5,33cdeccccebe80329f1fdbee7f5874cb", + "genome_mfa.CT_conversion.fa:md5,4dd181b65f1f3549f4132c9a3759eee8" + ], + [ + "BS_GA.1.ht2:md5,c2b02b7987f4ac0578332204678674cd", + "BS_GA.2.ht2:md5,579241d95941538b2e75bbdb6cfaa73d", + "BS_GA.3.ht2:md5,b41e72eefad74e8ede411c78a5bd5dee", + "BS_GA.4.ht2:md5,6b64fa496ffa2af2af235e1c87f06a25", + "BS_GA.5.ht2:md5,43aa1c78c6ec18c4165cf25159578fee", + "BS_GA.6.ht2:md5,2dc0f049d7d0f2a51822df8b195dce41", + "BS_GA.7.ht2:md5,9013eccd91ad614d7893c739275a394f", + "BS_GA.8.ht2:md5,33cdeccccebe80329f1fdbee7f5874cb", + "genome_mfa.GA_conversion.fa:md5,3dee732bc344fd620c3a7322f52c6a5f" + ] + ] + ] + ] + ], + [ + "versions.yml:md5,8e4e91d03b368e548eeafee8dd263e70" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-20T15:44:14.403574883" + }, + "Generate Bwameth Index": { + "content": [ + [ + [ + { + + }, + "/nf-core/test-datasets/raw/methylseq/reference/genome.fa" + ] + ], + [ + "genome.fa.fai:md5,84f5b44c25877ac58b154706cc8bc451" + ], + [ + [ + { + + }, + [ + "genome.fa.bwameth.c2t:md5,e51d48ed28fa0c26e2f9c9f13d09403b", + "genome.fa.bwameth.c2t.amb:md5,010a242c6764efb30141868a45d698b3", + "genome.fa.bwameth.c2t.ann:md5,09b4db3d87a2d4dac9e10e807f377110", + "genome.fa.bwameth.c2t.bwt:md5,4646f8ae6bd523b7f4106bbd32eff95e", + "genome.fa.bwameth.c2t.pac:md5,a662d7add09698e25c8152fd2306ec66", + "genome.fa.bwameth.c2t.sa:md5,4a1e905b828396a1909669bc9c573d8d" + ] + ] + ], + [ + "versions.yml:md5,7303f194674b485c6914e28422822a12", + "versions.yml:md5,cb3f3b6e54f9a7b3b6d4f5f875e89442" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-20T11:27:38.06274051" + }, + "Generate Bismark Index (bowtie2)": { + "content": [ + [ + [ + { + + }, + "/nf-core/test-datasets/raw/methylseq/reference/genome.fa" + ] + ], + [ + [ + { + + }, + [ + [ + [ + "BS_CT.1.bt2:md5,d53bef7d951c7d08e327944581c911eb", + "BS_CT.2.bt2:md5,752a03fc364115fc910e5a28ae154382", + "BS_CT.3.bt2:md5,b41e72eefad74e8ede411c78a5bd5dee", + "BS_CT.4.bt2:md5,02b3d1855a67fd9cbb4c411406a22fde", + "BS_CT.rev.1.bt2:md5,52ae603fff473b3b25eecd36c533edb9", + "BS_CT.rev.2.bt2:md5,0e290e05f7dae065cae54e29ed97afe5", + "genome_mfa.CT_conversion.fa:md5,4dd181b65f1f3549f4132c9a3759eee8" + ], + [ + "BS_GA.1.bt2:md5,9aff51b1712758b891b0c427a988977f", + "BS_GA.2.bt2:md5,579241d95941538b2e75bbdb6cfaa73d", + "BS_GA.3.bt2:md5,b41e72eefad74e8ede411c78a5bd5dee", + "BS_GA.4.bt2:md5,6b64fa496ffa2af2af235e1c87f06a25", + "BS_GA.rev.1.bt2:md5,dabf2d6f80ba7e8fc96dfdc203f6bbfd", + "BS_GA.rev.2.bt2:md5,fac2f8b39b0e15dec7aa79a0ecf12b49", + "genome_mfa.GA_conversion.fa:md5,3dee732bc344fd620c3a7322f52c6a5f" + ] + ] + ] + ] + ], + [ + "versions.yml:md5,8e4e91d03b368e548eeafee8dd263e70" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-20T11:27:14.196959225" + } +} \ No newline at end of file diff --git a/subworkflows/local/utils_nfcore_methylseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_methylseq_pipeline/main.nf new file mode 100644 index 00000000..f242fc0a --- /dev/null +++ b/subworkflows/local/utils_nfcore_methylseq_pipeline/main.nf @@ -0,0 +1,267 @@ +// +// Subworkflow with functionality specific to the nf-core/methylseq pipeline +// + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' +include { paramsSummaryMap } from 'plugin/nf-schema' +include { samplesheetToList } from 'plugin/nf-schema' +include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' +include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' +include { imNotification } from '../../nf-core/utils_nfcore_pipeline' +include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' +include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' +include { workflowCitation } from '../../nf-core/utils_nfcore_pipeline' + + + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + SUBWORKFLOW TO INITIALISE PIPELINE +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +workflow PIPELINE_INITIALISATION { + + take: + version // boolean: Display version and exit + validate_params // boolean: Boolean whether to validate parameters against the schema at runtime + monochrome_logs // boolean: Do not use coloured log outputs + nextflow_cli_args // array: List of positional nextflow CLI args + outdir // string: The output directory where the results will be saved + + main: + + ch_versions = Channel.empty() + + // + // Print version and exit if required and dump pipeline parameters to JSON file + // + UTILS_NEXTFLOW_PIPELINE ( + version, + true, + outdir, + workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1 + ) + + + // + // Validate parameters and generate parameter summary to stdout + // + UTILS_NFSCHEMA_PLUGIN ( + workflow, + validate_params, + null + ) + + + // + // Check config provided to the pipeline + // + UTILS_NFCORE_PIPELINE ( + nextflow_cli_args + ) + + // + // Custom validation for pipeline parameters + // + validateInputParameters() + + // + // Create channel from input file provided through params.input + // + + Channel + .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) + .map { + meta, fastq_1, fastq_2, genome -> + if (!fastq_2) { + return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ] + } else { + return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] + } + } + .groupTuple() + .map { samplesheet -> + validateInputSamplesheet(samplesheet) + } + .set { ch_samplesheet } + ch_samplesheet.dump(tag: "ch_samplesheet") + + emit: + samplesheet = ch_samplesheet + versions = ch_versions +} + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + SUBWORKFLOW FOR PIPELINE COMPLETION +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +workflow PIPELINE_COMPLETION { + + take: + email // string: email address + email_on_fail // string: email address sent on pipeline failure + plaintext_email // boolean: Send plain-text email instead of HTML + + outdir // path: Path to output directory where results will be published + monochrome_logs // boolean: Disable ANSI colour codes in log output + hook_url // string: hook URL for notifications + multiqc_report // string: Path to MultiQC report + + main: + summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") + + // + // Completion email and summary + // + workflow.onComplete { + if (email || email_on_fail) { + completionEmail( + summary_params, + email, + email_on_fail, + plaintext_email, + outdir, + monochrome_logs, + multiqc_report.toList() + ) + } + + completionSummary(monochrome_logs) + if (hook_url) { + imNotification(summary_params, hook_url) + } + } + + workflow.onError { + log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting" + } +} + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + FUNCTIONS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ +// +// Check and validate pipeline parameters +// +def validateInputParameters() { + genomeExistsError() +} + +// +// Validate channels from input samplesheet +// +def validateInputSamplesheet(input) { + def (metas, fastqs) = input[1..2] + + // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end + def endedness_ok = metas.collect{ meta -> meta.single_end }.unique().size == 1 + if (!endedness_ok) { + error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}") + } + + return [ metas[0], fastqs ] +} +// +// Get attribute from genome config file e.g. fasta +// +def getGenomeAttribute(attribute) { + if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) { + if (params.genomes[ params.genome ].containsKey(attribute)) { + return params.genomes[ params.genome ][ attribute ] + } + } + return null +} + +// +// Exit pipeline if incorrect --genome key provided +// +def genomeExistsError() { + if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { + def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + + " Currently, the available genome keys are:\n" + + " ${params.genomes.keySet().join(", ")}\n" + + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + error(error_string) + } +} +// +// Generate methods description for MultiQC +// +def toolCitationText() { + // FIXME Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", + def citation_text = [ + "Tools used in the workflow included:", + "FastQC (Andrews 2010),", + "Trim Galore! (Krueger)", + "Bismark (Krueger 2011)", + "bwa-meth (Pedersen 2014)", + "Picard (Broad Institute 2019)", + "Qualimap (Okonechnikov 2015)", + "Preseq (Daley 2013)", + "MultiQC (Ewels et al. 2016)", + "." + ].join(' ').trim() +} + +def toolBibliographyText() { + // FIXME Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "
  • Author (2023) Pub name, Journal, DOI
    • " : "", + def reference_text = [ + "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).", + "Ewels, P., Magnusson, M., Lundin, S., & KΓ€ller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354", + "https://www.bioinformatics.babraham.ac.uk/projects/trim_galore", + "Felix Krueger, Simon R. Andrews, Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications, Bioinformatics, Volume 27, Issue 11, 1 June 2011, Pages 1571–1572, doi: /10.1093/bioinformatics/btr167", + "Pedersen, Brent S. and Eyring, Kenneth and De, Subhajyoti and Yang, Ivana V. and Schwartz, David A. Fast and accurate alignment of long bisulfite-seq reads, arXiv:1401.1129, doi: 10.48550/arXiv.1401.1129", + "Picard Tools, Broad Institute. ", + "Konstantin Okonechnikov, Ana Conesa, Fernando GarcΓ­a-Alcalde, Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data, Bioinformatics, Volume 32, Issue 2, 15 January 2016, Pages 292–294, doi: 10.1093/bioinformatics/btv566", + "Daley, T., Smith, A. Predicting the molecular complexity of sequencing libraries. Nat Methods 10, 325–327 (2013). doi: 10.1038/nmeth.2375
    • ", + ].join('
  • ').trim() + + return reference_text +} + +def methodsDescriptionText(mqc_methods_yaml) { + // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file + def meta = [:] + meta.workflow = workflow.toMap() + meta["manifest_map"] = workflow.manifest.toMap() + + // Pipeline DOI + if (meta.manifest_map.doi) { + // Using a loop to handle multiple DOIs + // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers + // Removing ` ` since the manifest.doi is a string and not a proper list + def temp_doi_ref = "" + def manifest_doi = meta.manifest_map.doi.tokenize(",") + manifest_doi.each { doi_ref -> + temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " + } + meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2) + } else meta["doi_text"] = "" + meta["nodoi_text"] = meta.manifest_map.doi ? "" : "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " + + // Tool references + meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") + meta["tool_bibliography"] = toolBibliographyText() + + + def methods_text = mqc_methods_yaml.text + + def engine = new groovy.text.SimpleTemplateEngine() + def description_html = engine.createTemplate(methods_text).make(meta) + + return description_html.toString() +} + diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf new file mode 100644 index 00000000..0fcbf7b3 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -0,0 +1,124 @@ +// +// Subworkflow with functionality that may be useful for any Nextflow pipeline +// + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + SUBWORKFLOW DEFINITION +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +workflow UTILS_NEXTFLOW_PIPELINE { + take: + print_version // boolean: print version + dump_parameters // boolean: dump parameters + outdir // path: base directory used to publish pipeline results + check_conda_channels // boolean: check conda channels + + main: + + // + // Print workflow version and exit on --version + // + if (print_version) { + log.info("${workflow.manifest.name} ${getWorkflowVersion()}") + System.exit(0) + } + + // + // Dump pipeline parameters to a JSON file + // + if (dump_parameters && outdir) { + dumpParametersToJSON(outdir) + } + + // + // When running with Conda, warn if channels have not been set-up appropriately + // + if (check_conda_channels) { + checkCondaChannels() + } + + emit: + dummy_emit = true +} + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + FUNCTIONS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +// +// Generate version string +// +def getWorkflowVersion() { + def version_string = "" as String + if (workflow.manifest.version) { + def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' + version_string += "${prefix_v}${workflow.manifest.version}" + } + + if (workflow.commitId) { + def git_shortsha = workflow.commitId.substring(0, 7) + version_string += "-g${git_shortsha}" + } + + return version_string +} + +// +// Dump pipeline parameters to a JSON file +// +def dumpParametersToJSON(outdir) { + def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss') + def filename = "params_${timestamp}.json" + def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") + def jsonStr = groovy.json.JsonOutput.toJson(params) + temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) + + nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") + temp_pf.delete() +} + +// +// When running with -profile conda, warn if channels have not been set-up appropriately +// +def checkCondaChannels() { + def parser = new org.yaml.snakeyaml.Yaml() + def channels = [] + try { + def config = parser.load("conda config --show channels".execute().text) + channels = config.channels + } + catch (NullPointerException e) { + log.warn("Could not verify conda channel configuration.") + return null + } + catch (IOException e) { + log.warn("Could not verify conda channel configuration.") + return null + } + + // Check that all channels are present + // This channel list is ordered by required channel priority. + def required_channels_in_order = ['conda-forge', 'bioconda'] + def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean + + // Check that they are in the right order + def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order } + + if (channels_missing | channel_priority_violation) { + log.warn """\ + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + There is a problem with your Conda configuration! + You will need to set-up the conda-forge and bioconda channels correctly. + Please refer to https://bioconda.github.io/ + The observed channel order is + ${channels} + but the following channel order is required: + ${required_channels_in_order} + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + """.stripIndent(true) + } +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml new file mode 100644 index 00000000..e5c3a0a8 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml @@ -0,0 +1,38 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "UTILS_NEXTFLOW_PIPELINE" +description: Subworkflow with functionality that may be useful for any Nextflow pipeline +keywords: + - utility + - pipeline + - initialise + - version +components: [] +input: + - print_version: + type: boolean + description: | + Print the version of the pipeline and exit + - dump_parameters: + type: boolean + description: | + Dump the parameters of the pipeline to a JSON file + - output_directory: + type: directory + description: Path to output dir to write JSON file to. + pattern: "results/" + - check_conda_channel: + type: boolean + description: | + Check if the conda channel priority is correct. +output: + - dummy_emit: + type: boolean + description: | + Dummy emit to make nf-core subworkflows lint happy +authors: + - "@adamrtalbot" + - "@drpatelh" +maintainers: + - "@adamrtalbot" + - "@drpatelh" + - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test new file mode 100644 index 00000000..68718e4f --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test @@ -0,0 +1,54 @@ + +nextflow_function { + + name "Test Functions" + script "subworkflows/nf-core/utils_nextflow_pipeline/main.nf" + config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config" + tag 'subworkflows' + tag 'utils_nextflow_pipeline' + tag 'subworkflows/utils_nextflow_pipeline' + + test("Test Function getWorkflowVersion") { + + function "getWorkflowVersion" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function dumpParametersToJSON") { + + function "dumpParametersToJSON" + + when { + function { + """ + // define inputs of the function here. Example: + input[0] = "$outputDir" + """.stripIndent() + } + } + + then { + assertAll( + { assert function.success } + ) + } + } + + test("Test Function checkCondaChannels") { + + function "checkCondaChannels" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap new file mode 100644 index 00000000..e3f0baf4 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap @@ -0,0 +1,20 @@ +{ + "Test Function getWorkflowVersion": { + "content": [ + "v9.9.9" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:05.308243" + }, + "Test Function checkCondaChannels": { + "content": null, + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:12.425833" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test new file mode 100644 index 00000000..ca964ce8 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -0,0 +1,111 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NEXTFLOW_PIPELINE" + script "../main.nf" + config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config" + workflow "UTILS_NEXTFLOW_PIPELINE" + tag 'subworkflows' + tag 'utils_nextflow_pipeline' + tag 'subworkflows/utils_nextflow_pipeline' + + test("Should run no inputs") { + + when { + workflow { + """ + print_version = false + dump_parameters = false + outdir = null + check_conda_channels = false + + input[0] = print_version + input[1] = dump_parameters + input[2] = outdir + input[3] = check_conda_channels + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should print version") { + + when { + workflow { + """ + print_version = true + dump_parameters = false + outdir = null + check_conda_channels = false + + input[0] = print_version + input[1] = dump_parameters + input[2] = outdir + input[3] = check_conda_channels + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.stdout.contains("nextflow_workflow v9.9.9") } + ) + } + } + + test("Should dump params") { + + when { + workflow { + """ + print_version = false + dump_parameters = true + outdir = 'results' + check_conda_channels = false + + input[0] = false + input[1] = true + input[2] = outdir + input[3] = false + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should not create params JSON if no output directory") { + + when { + workflow { + """ + print_version = false + dump_parameters = true + outdir = null + check_conda_channels = false + + input[0] = false + input[1] = true + input[2] = outdir + input[3] = false + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config new file mode 100644 index 00000000..a09572e5 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -0,0 +1,9 @@ +manifest { + name = 'nextflow_workflow' + author = """nf-core""" + homePage = 'https://127.0.0.1' + description = """Dummy pipeline""" + nextflowVersion = '!>=23.04.0' + version = '9.9.9' + doi = 'https://doi.org/10.5281/zenodo.5070524' +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml new file mode 100644 index 00000000..f8476112 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/utils_nextflow_pipeline: + - subworkflows/nf-core/utils_nextflow_pipeline/** diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf new file mode 100644 index 00000000..5cb7bafe --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -0,0 +1,462 @@ +// +// Subworkflow with utility functions specific to the nf-core pipeline template +// + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + SUBWORKFLOW DEFINITION +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +workflow UTILS_NFCORE_PIPELINE { + take: + nextflow_cli_args + + main: + valid_config = checkConfigProvided() + checkProfileProvided(nextflow_cli_args) + + emit: + valid_config +} + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + FUNCTIONS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +// +// Warn if a -profile or Nextflow config has not been provided to run the pipeline +// +def checkConfigProvided() { + def valid_config = true as Boolean + if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { + log.warn( + "[${workflow.manifest.name}] You are attempting to run the pipeline without any custom configuration!\n\n" + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + "Please refer to the quick start section and usage docs for the pipeline.\n " + ) + valid_config = false + } + return valid_config +} + +// +// Exit pipeline if --profile contains spaces +// +def checkProfileProvided(nextflow_cli_args) { + if (workflow.profile.endsWith(',')) { + error( + "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + ) + } + if (nextflow_cli_args[0]) { + log.warn( + "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + ) + } +} + +// +// Citation string for pipeline +// +def workflowCitation() { + def temp_doi_ref = "" + def manifest_doi = workflow.manifest.doi.tokenize(",") + // Handling multiple DOIs + // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers + // Removing ` ` since the manifest.doi is a string and not a proper list + manifest_doi.each { doi_ref -> + temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" + } + return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + "* The nf-core framework\n" + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" +} + +// +// Generate workflow version string +// +def getWorkflowVersion() { + def version_string = "" as String + if (workflow.manifest.version) { + def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' + version_string += "${prefix_v}${workflow.manifest.version}" + } + + if (workflow.commitId) { + def git_shortsha = workflow.commitId.substring(0, 7) + version_string += "-g${git_shortsha}" + } + + return version_string +} + +// +// Get software versions for pipeline +// +def processVersionsFromYAML(yaml_file) { + def yaml = new org.yaml.snakeyaml.Yaml() + def versions = yaml.load(yaml_file).collectEntries { k, v -> [k.tokenize(':')[-1], v] } + return yaml.dumpAsMap(versions).trim() +} + +// +// Get workflow version for pipeline +// +def workflowVersionToYAML() { + return """ + Workflow: + ${workflow.manifest.name}: ${getWorkflowVersion()} + Nextflow: ${workflow.nextflow.version} + """.stripIndent().trim() +} + +// +// Get channel of software versions used in pipeline in YAML format +// +def softwareVersionsToYAML(ch_versions) { + return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML())) +} + +// +// Get workflow summary for MultiQC +// +def paramsSummaryMultiqc(summary_params) { + def summary_section = '' + summary_params + .keySet() + .each { group -> + def group_params = summary_params.get(group) + // This gets the parameters of that particular group + if (group_params) { + summary_section += "

    ${group}

    \n" + summary_section += "
    \n" + group_params + .keySet() + .sort() + .each { param -> + summary_section += "
    ${param}
    ${group_params.get(param) ?: 'N/A'}
    \n" + } + summary_section += "
    \n" + } + } + + def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String + yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" + yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" + yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" + yaml_file_text += "plot_type: 'html'\n" + yaml_file_text += "data: |\n" + yaml_file_text += "${summary_section}" + + return yaml_file_text +} + +// +// nf-core logo +// +def nfCoreLogo(monochrome_logs=true) { + def colors = logColours(monochrome_logs) as Map + String.format( + """\n + ${dashedLine(monochrome_logs)} + ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} + ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} + ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} + ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} + ${colors.green}`._,._,\'${colors.reset} + ${colors.purple} ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset} + ${dashedLine(monochrome_logs)} + """.stripIndent() + ) +} + +// +// Return dashed line +// +def dashedLine(monochrome_logs=true) { + def colors = logColours(monochrome_logs) as Map + return "-${colors.dim}----------------------------------------------------${colors.reset}-" +} + +// +// ANSII colours used for terminal logging +// +def logColours(monochrome_logs=true) { + def colorcodes = [:] as Map + + // Reset / Meta + colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" + colorcodes['bold'] = monochrome_logs ? '' : "\033[1m" + colorcodes['dim'] = monochrome_logs ? '' : "\033[2m" + colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m" + colorcodes['blink'] = monochrome_logs ? '' : "\033[5m" + colorcodes['reverse'] = monochrome_logs ? '' : "\033[7m" + colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" + + // Regular Colors + colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" + colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" + colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" + colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" + colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" + colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" + colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" + colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" + + // Bold + colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" + colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" + colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" + colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" + colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" + colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" + colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" + colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" + + // Underline + colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" + colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" + colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" + colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" + colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" + colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" + colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" + colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" + + // High Intensity + colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" + colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" + colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" + colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" + colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" + colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" + colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" + colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" + + // Bold High Intensity + colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" + colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" + colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" + colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" + colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" + colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" + colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" + colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" + + return colorcodes +} + +// +// Attach the multiqc report to email +// +def attachMultiqcReport(multiqc_report) { + def mqc_report = null + try { + if (workflow.success) { + mqc_report = multiqc_report.getVal() + if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { + if (mqc_report.size() > 1) { + log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one") + } + mqc_report = mqc_report[0] + } + } + } + catch (Exception all) { + if (multiqc_report) { + log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email") + } + } + return mqc_report +} + +// +// Construct and send completion email +// +def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) { + + // Set up the e-mail variables + def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}" + if (!workflow.success) { + subject = "[${workflow.manifest.name}] FAILED: ${workflow.runName}" + } + + def summary = [:] + summary_params + .keySet() + .sort() + .each { group -> + summary << summary_params[group] + } + + def misc_fields = [:] + misc_fields['Date Started'] = workflow.start + misc_fields['Date Completed'] = workflow.complete + misc_fields['Pipeline script file path'] = workflow.scriptFile + misc_fields['Pipeline script hash ID'] = workflow.scriptId + if (workflow.repository) { + misc_fields['Pipeline repository Git URL'] = workflow.repository + } + if (workflow.commitId) { + misc_fields['Pipeline repository Git Commit'] = workflow.commitId + } + if (workflow.revision) { + misc_fields['Pipeline Git branch/tag'] = workflow.revision + } + misc_fields['Nextflow Version'] = workflow.nextflow.version + misc_fields['Nextflow Build'] = workflow.nextflow.build + misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp + + def email_fields = [:] + email_fields['version'] = getWorkflowVersion() + email_fields['runName'] = workflow.runName + email_fields['success'] = workflow.success + email_fields['dateComplete'] = workflow.complete + email_fields['duration'] = workflow.duration + email_fields['exitStatus'] = workflow.exitStatus + email_fields['errorMessage'] = (workflow.errorMessage ?: 'None') + email_fields['errorReport'] = (workflow.errorReport ?: 'None') + email_fields['commandLine'] = workflow.commandLine + email_fields['projectDir'] = workflow.projectDir + email_fields['summary'] = summary << misc_fields + + // On success try attach the multiqc report + def mqc_report = attachMultiqcReport(multiqc_report) + + // Check if we are only sending emails on failure + def email_address = email + if (!email && email_on_fail && !workflow.success) { + email_address = email_on_fail + } + + // Render the TXT template + def engine = new groovy.text.GStringTemplateEngine() + def tf = new File("${workflow.projectDir}/assets/email_template.txt") + def txt_template = engine.createTemplate(tf).make(email_fields) + def email_txt = txt_template.toString() + + // Render the HTML template + def hf = new File("${workflow.projectDir}/assets/email_template.html") + def html_template = engine.createTemplate(hf).make(email_fields) + def email_html = html_template.toString() + + // Render the sendmail template + def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit + def smail_fields = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()] + def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt") + def sendmail_template = engine.createTemplate(sf).make(smail_fields) + def sendmail_html = sendmail_template.toString() + + // Send the HTML e-mail + def colors = logColours(monochrome_logs) as Map + if (email_address) { + try { + if (plaintext_email) { +new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } + // Try to send HTML e-mail using sendmail + def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") + sendmail_tf.withWriter { w -> w << sendmail_html } + ['sendmail', '-t'].execute() << sendmail_html + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-") + } + catch (Exception all) { + // Catch failures and try with plaintext + def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address] + mail_cmd.execute() << email_html + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (mail)-") + } + } + + // Write summary e-mail HTML to a file + def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") + output_hf.withWriter { w -> w << email_html } + nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html") + output_hf.delete() + + // Write summary e-mail TXT to a file + def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") + output_tf.withWriter { w -> w << email_txt } + nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt") + output_tf.delete() +} + +// +// Print pipeline summary on completion +// +def completionSummary(monochrome_logs=true) { + def colors = logColours(monochrome_logs) as Map + if (workflow.success) { + if (workflow.stats.ignoredCount == 0) { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Pipeline completed successfully${colors.reset}-") + } + else { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-") + } + } + else { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-") + } +} + +// +// Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack +// +def imNotification(summary_params, hook_url) { + def summary = [:] + summary_params + .keySet() + .sort() + .each { group -> + summary << summary_params[group] + } + + def misc_fields = [:] + misc_fields['start'] = workflow.start + misc_fields['complete'] = workflow.complete + misc_fields['scriptfile'] = workflow.scriptFile + misc_fields['scriptid'] = workflow.scriptId + if (workflow.repository) { + misc_fields['repository'] = workflow.repository + } + if (workflow.commitId) { + misc_fields['commitid'] = workflow.commitId + } + if (workflow.revision) { + misc_fields['revision'] = workflow.revision + } + misc_fields['nxf_version'] = workflow.nextflow.version + misc_fields['nxf_build'] = workflow.nextflow.build + misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp + + def msg_fields = [:] + msg_fields['version'] = getWorkflowVersion() + msg_fields['runName'] = workflow.runName + msg_fields['success'] = workflow.success + msg_fields['dateComplete'] = workflow.complete + msg_fields['duration'] = workflow.duration + msg_fields['exitStatus'] = workflow.exitStatus + msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') + msg_fields['errorReport'] = (workflow.errorReport ?: 'None') + msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") + msg_fields['projectDir'] = workflow.projectDir + msg_fields['summary'] = summary << misc_fields + + // Render the JSON template + def engine = new groovy.text.GStringTemplateEngine() + // Different JSON depending on the service provider + // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format + def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" + def hf = new File("${workflow.projectDir}/assets/${json_path}") + def json_template = engine.createTemplate(hf).make(msg_fields) + def json_message = json_template.toString() + + // POST + def post = new URL(hook_url).openConnection() + post.setRequestMethod("POST") + post.setDoOutput(true) + post.setRequestProperty("Content-Type", "application/json") + post.getOutputStream().write(json_message.getBytes("UTF-8")) + def postRC = post.getResponseCode() + if (!postRC.equals(200)) { + log.warn(post.getErrorStream().getText()) + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml new file mode 100644 index 00000000..d08d2434 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml @@ -0,0 +1,24 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "UTILS_NFCORE_PIPELINE" +description: Subworkflow with utility functions specific to the nf-core pipeline template +keywords: + - utility + - pipeline + - initialise + - version +components: [] +input: + - nextflow_cli_args: + type: list + description: | + Nextflow CLI positional arguments +output: + - success: + type: boolean + description: | + Dummy output to indicate success +authors: + - "@adamrtalbot" +maintainers: + - "@adamrtalbot" + - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test new file mode 100644 index 00000000..1dc317f8 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test @@ -0,0 +1,134 @@ + +nextflow_function { + + name "Test Functions" + script "../main.nf" + config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "utils_nfcore_pipeline" + tag "subworkflows/utils_nfcore_pipeline" + + test("Test Function checkConfigProvided") { + + function "checkConfigProvided" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function checkProfileProvided") { + + function "checkProfileProvided" + + when { + function { + """ + input[0] = [] + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function workflowCitation") { + + function "workflowCitation" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function nfCoreLogo") { + + function "nfCoreLogo" + + when { + function { + """ + input[0] = false + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function dashedLine") { + + function "dashedLine" + + when { + function { + """ + input[0] = false + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function without logColours") { + + function "logColours" + + when { + function { + """ + input[0] = true + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function with logColours") { + function "logColours" + + when { + function { + """ + input[0] = false + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap new file mode 100644 index 00000000..1037232c --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap @@ -0,0 +1,166 @@ +{ + "Test Function checkProfileProvided": { + "content": null, + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:03.360873" + }, + "Test Function checkConfigProvided": { + "content": [ + true + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:59.729647" + }, + "Test Function nfCoreLogo": { + "content": [ + "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:10.562934" + }, + "Test Function workflowCitation": { + "content": [ + "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n https://github.com/nextflow_workflow/blob/master/CITATIONS.md" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:07.019761" + }, + "Test Function without logColours": { + "content": [ + { + "reset": "", + "bold": "", + "dim": "", + "underlined": "", + "blink": "", + "reverse": "", + "hidden": "", + "black": "", + "red": "", + "green": "", + "yellow": "", + "blue": "", + "purple": "", + "cyan": "", + "white": "", + "bblack": "", + "bred": "", + "bgreen": "", + "byellow": "", + "bblue": "", + "bpurple": "", + "bcyan": "", + "bwhite": "", + "ublack": "", + "ured": "", + "ugreen": "", + "uyellow": "", + "ublue": "", + "upurple": "", + "ucyan": "", + "uwhite": "", + "iblack": "", + "ired": "", + "igreen": "", + "iyellow": "", + "iblue": "", + "ipurple": "", + "icyan": "", + "iwhite": "", + "biblack": "", + "bired": "", + "bigreen": "", + "biyellow": "", + "biblue": "", + "bipurple": "", + "bicyan": "", + "biwhite": "" + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:17.969323" + }, + "Test Function dashedLine": { + "content": [ + "-\u001b[2m----------------------------------------------------\u001b[0m-" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:14.366181" + }, + "Test Function with logColours": { + "content": [ + { + "reset": "\u001b[0m", + "bold": "\u001b[1m", + "dim": "\u001b[2m", + "underlined": "\u001b[4m", + "blink": "\u001b[5m", + "reverse": "\u001b[7m", + "hidden": "\u001b[8m", + "black": "\u001b[0;30m", + "red": "\u001b[0;31m", + "green": "\u001b[0;32m", + "yellow": "\u001b[0;33m", + "blue": "\u001b[0;34m", + "purple": "\u001b[0;35m", + "cyan": "\u001b[0;36m", + "white": "\u001b[0;37m", + "bblack": "\u001b[1;30m", + "bred": "\u001b[1;31m", + "bgreen": "\u001b[1;32m", + "byellow": "\u001b[1;33m", + "bblue": "\u001b[1;34m", + "bpurple": "\u001b[1;35m", + "bcyan": "\u001b[1;36m", + "bwhite": "\u001b[1;37m", + "ublack": "\u001b[4;30m", + "ured": "\u001b[4;31m", + "ugreen": "\u001b[4;32m", + "uyellow": "\u001b[4;33m", + "ublue": "\u001b[4;34m", + "upurple": "\u001b[4;35m", + "ucyan": "\u001b[4;36m", + "uwhite": "\u001b[4;37m", + "iblack": "\u001b[0;90m", + "ired": "\u001b[0;91m", + "igreen": "\u001b[0;92m", + "iyellow": "\u001b[0;93m", + "iblue": "\u001b[0;94m", + "ipurple": "\u001b[0;95m", + "icyan": "\u001b[0;96m", + "iwhite": "\u001b[0;97m", + "biblack": "\u001b[1;90m", + "bired": "\u001b[1;91m", + "bigreen": "\u001b[1;92m", + "biyellow": "\u001b[1;93m", + "biblue": "\u001b[1;94m", + "bipurple": "\u001b[1;95m", + "bicyan": "\u001b[1;96m", + "biwhite": "\u001b[1;97m" + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:21.714424" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test new file mode 100644 index 00000000..8940d32d --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test @@ -0,0 +1,29 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NFCORE_PIPELINE" + script "../main.nf" + config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" + workflow "UTILS_NFCORE_PIPELINE" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "utils_nfcore_pipeline" + tag "subworkflows/utils_nfcore_pipeline" + + test("Should run without failures") { + + when { + workflow { + """ + input[0] = [] + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap new file mode 100644 index 00000000..859d1030 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap @@ -0,0 +1,19 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + true + ], + "valid_config": [ + true + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:25.726491" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config new file mode 100644 index 00000000..d0a926bf --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config @@ -0,0 +1,9 @@ +manifest { + name = 'nextflow_workflow' + author = """nf-core""" + homePage = 'https://127.0.0.1' + description = """Dummy pipeline""" + nextflowVersion = '!>=23.04.0' + version = '9.9.9' + doi = 'https://doi.org/10.5281/zenodo.5070524' +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml new file mode 100644 index 00000000..ac8523c9 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/utils_nfcore_pipeline: + - subworkflows/nf-core/utils_nfcore_pipeline/** diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf new file mode 100644 index 00000000..4994303e --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -0,0 +1,46 @@ +// +// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary +// + +include { paramsSummaryLog } from 'plugin/nf-schema' +include { validateParameters } from 'plugin/nf-schema' + +workflow UTILS_NFSCHEMA_PLUGIN { + + take: + input_workflow // workflow: the workflow object used by nf-schema to get metadata from the workflow + validate_params // boolean: validate the parameters + parameters_schema // string: path to the parameters JSON schema. + // this has to be the same as the schema given to `validation.parametersSchema` + // when this input is empty it will automatically use the configured schema or + // "${projectDir}/nextflow_schema.json" as default. This input should not be empty + // for meta pipelines + + main: + + // + // Print parameter summary to stdout. This will display the parameters + // that differ from the default given in the JSON schema + // + if(parameters_schema) { + log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema) + } else { + log.info paramsSummaryLog(input_workflow) + } + + // + // Validate the parameters using nextflow_schema.json or the schema + // given via the validation.parametersSchema configuration option + // + if(validate_params) { + if(parameters_schema) { + validateParameters(parameters_schema:parameters_schema) + } else { + validateParameters() + } + } + + emit: + dummy_emit = true +} + diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml new file mode 100644 index 00000000..f7d9f028 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml @@ -0,0 +1,35 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "utils_nfschema_plugin" +description: Run nf-schema to validate parameters and create a summary of changed parameters +keywords: + - validation + - JSON schema + - plugin + - parameters + - summary +components: [] +input: + - input_workflow: + type: object + description: | + The workflow object of the used pipeline. + This object contains meta data used to create the params summary log + - validate_params: + type: boolean + description: Validate the parameters and error if invalid. + - parameters_schema: + type: string + description: | + Path to the parameters JSON schema. + This has to be the same as the schema given to the `validation.parametersSchema` config + option. When this input is empty it will automatically use the configured schema or + "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way + for meta pipelines. +output: + - dummy_emit: + type: boolean + description: Dummy emit to make nf-core subworkflows lint happy +authors: + - "@nvnieuwk" +maintainers: + - "@nvnieuwk" diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test new file mode 100644 index 00000000..842dc432 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -0,0 +1,117 @@ +nextflow_workflow { + + name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN" + script "../main.nf" + workflow "UTILS_NFSCHEMA_PLUGIN" + + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/utils_nfschema_plugin" + tag "plugin/nf-schema" + + config "./nextflow.config" + + test("Should run nothing") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "" + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params") { + + when { + + params { + test_data = '' + outdir = 1 + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "" + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } + + test("Should run nothing - custom schema") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params - custom schema") { + + when { + + params { + test_data = '' + outdir = 1 + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config new file mode 100644 index 00000000..0907ac58 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -0,0 +1,8 @@ +plugins { + id "nf-schema@2.1.0" +} + +validation { + parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + monochromeLogs = true +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json new file mode 100644 index 00000000..331e0d2f --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json @@ -0,0 +1,96 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", + "title": ". pipeline parameters", + "description": "", + "type": "object", + "$defs": { + "input_output_options": { + "title": "Input/output options", + "type": "object", + "fa_icon": "fas fa-terminal", + "description": "Define where the pipeline should find input data and save output data.", + "required": ["outdir"], + "properties": { + "validate_params": { + "type": "boolean", + "description": "Validate parameters?", + "default": true, + "hidden": true + }, + "outdir": { + "type": "string", + "format": "directory-path", + "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.", + "fa_icon": "fas fa-folder-open" + }, + "test_data_base": { + "type": "string", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules", + "description": "Base for test data directory", + "hidden": true + }, + "test_data": { + "type": "string", + "description": "Fake test data param", + "hidden": true + } + } + }, + "generic_options": { + "title": "Generic options", + "type": "object", + "fa_icon": "fas fa-file-import", + "description": "Less common options for the pipeline, typically set in a config file.", + "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", + "properties": { + "help": { + "type": "boolean", + "description": "Display help text.", + "fa_icon": "fas fa-question-circle", + "hidden": true + }, + "version": { + "type": "boolean", + "description": "Display version and exit.", + "fa_icon": "fas fa-question-circle", + "hidden": true + }, + "logo": { + "type": "boolean", + "default": true, + "description": "Display nf-core logo in console output.", + "fa_icon": "fas fa-image", + "hidden": true + }, + "singularity_pull_docker_container": { + "type": "boolean", + "description": "Pull Singularity container from Docker?", + "hidden": true + }, + "publish_dir_mode": { + "type": "string", + "default": "copy", + "description": "Method used to save pipeline results to output directory.", + "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", + "fa_icon": "fas fa-copy", + "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], + "hidden": true + }, + "monochrome_logs": { + "type": "boolean", + "description": "Use monochrome_logs", + "hidden": true + } + } + } + }, + "allOf": [ + { + "$ref": "#/$defs/input_output_options" + }, + { + "$ref": "#/$defs/generic_options" + } + ] +} diff --git a/tests/.nftignore b/tests/.nftignore new file mode 100644 index 00000000..7c0558cf --- /dev/null +++ b/tests/.nftignore @@ -0,0 +1,23 @@ +{bismark,bismark_hisat}/alignments/logs/*.txt +{bismark,bismark_hisat,bwameth}/{alignments,deduplicated}/*.{bam,bam.bai} +{bismark,bismark_hisat}/deduplicated/logs/*.txt +{bismark,bismark_hisat}/{reports,summary}/*.{html,txt} +bwameth/deduplicated/picard_metrics/*.txt +fastqc/*.html +fastqc/zips/*.zip +multiqc/{bismark,bismark_hisat,bwameth}/multiqc_data/*.{log,json} +multiqc/{bismark,bismark_hisat,bwameth}/multiqc_data/multiqc_fastqc.txt +multiqc/{bismark,bismark_hisat,bwameth}/multiqc_data/multiqc_general_stats.txt +multiqc/{bismark,bismark_hisat,bwameth}/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt +multiqc/{bismark,bismark_hisat,bwameth}/multiqc_data/multiqc_software_versions.txt +multiqc/{bismark,bismark_hisat,bwameth}/multiqc_data/multiqc_sources.txt +multiqc/{bismark,bismark_hisat,bwameth}/multiqc_report.html +multiqc/{bismark,bismark_hisat,bwameth}/multiqc_plots/{pdf,png,svg}/*.{pdf,png,svg} +pipeline_info/*.{html,json,txt,yml} +qualimap/**/qualimapReport.html +qualimap/**/css/* +qualimap/**/images_qualimapReport/* +qualimap/**/raw_data_qualimapReport/* +trimgalore/fastqc/*.html +trimgalore/fastqc/zips/*.zip +trimgalore/logs/*.txt diff --git a/tests/bismark_emseq_clip_r1.nf.test b/tests/bismark_emseq_clip_r1.nf.test new file mode 100644 index 00000000..c1bc57a0 --- /dev/null +++ b/tests/bismark_emseq_clip_r1.nf.test @@ -0,0 +1,41 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "../main.nf" + config "./nextflow.config" + + test("Params: bismark | em_seq | clip_r1") { + when { + params { + em_seq = true + clip_r1 = 2 + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name + stable_name, + // All files with stable contents + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + ).match() } + ) + } + } + +} diff --git a/tests/bismark_emseq_clip_r1.nf.test.snap b/tests/bismark_emseq_clip_r1.nf.test.snap new file mode 100644 index 00000000..0f82b86b --- /dev/null +++ b/tests/bismark_emseq_clip_r1.nf.test.snap @@ -0,0 +1,579 @@ +{ + "Params: bismark | em_seq | clip_r1": { + "content": [ + 43, + { + "BISMARK_ALIGN": { + "bismark": "0.24.2" + }, + "BISMARK_GENOMEPREPARATION": { + "bismark": "0.24.2" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "QUALIMAP_BAMQC": { + "qualimap": 2.3 + }, + "TRIMGALORE": { + "trimgalore": "0.6.10", + "cutadapt": 4.2 + }, + "Workflow": { + "nf-core/methylseq": "v2.7.0" + } + }, + [ + "bismark", + "bismark/alignments", + "bismark/alignments/logs", + "bismark/alignments/logs/Ecoli_10K_methylated_1_val_1_bismark_bt2_PE_report.txt", + "bismark/alignments/logs/SRR389222_sub1_trimmed_bismark_bt2_SE_report.txt", + "bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt", + "bismark/alignments/logs/SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt", + "bismark/deduplicated", + "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", + "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", + "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", + "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", + "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam.bai", + "bismark/deduplicated/logs", + "bismark/deduplicated/logs/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplication_report.txt", + "bismark/deduplicated/logs/SRR389222_sub1_trimmed_bismark_bt2.deduplication_report.txt", + "bismark/deduplicated/logs/SRR389222_sub2_trimmed_bismark_bt2.deduplication_report.txt", + "bismark/deduplicated/logs/SRR389222_sub3_trimmed_bismark_bt2.deduplication_report.txt", + "bismark/methylation_calls", + "bismark/methylation_calls/bedGraph", + "bismark/methylation_calls/bedGraph/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz", + "bismark/methylation_calls/bedGraph/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bedGraph.gz", + "bismark/methylation_calls/bedGraph/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bedGraph.gz", + "bismark/methylation_calls/bedGraph/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bedGraph.gz", + "bismark/methylation_calls/mbias", + "bismark/methylation_calls/mbias/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt", + "bismark/methylation_calls/mbias/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.M-bias.txt", + "bismark/methylation_calls/mbias/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.M-bias.txt", + "bismark/methylation_calls/mbias/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.M-bias.txt", + "bismark/methylation_calls/methylation_calls", + "bismark/methylation_calls/methylation_calls/CHG_OB_Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplicated.txt.gz", + "bismark/methylation_calls/methylation_calls/CHG_OB_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz", + "bismark/methylation_calls/methylation_calls/CHG_OB_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz", + "bismark/methylation_calls/methylation_calls/CHG_OB_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz", + "bismark/methylation_calls/methylation_calls/CHG_OT_Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplicated.txt.gz", + 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"bismark/methylation_calls/methylation_calls/CHH_OT_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz", + "bismark/methylation_calls/methylation_calls/CHH_OT_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz", + "bismark/methylation_calls/methylation_calls/CHH_OT_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz", + "bismark/methylation_calls/methylation_calls/CpG_OB_Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplicated.txt.gz", + "bismark/methylation_calls/methylation_calls/CpG_OB_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz", + "bismark/methylation_calls/methylation_calls/CpG_OB_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz", + "bismark/methylation_calls/methylation_calls/CpG_OB_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz", + "bismark/methylation_calls/methylation_calls/CpG_OT_Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplicated.txt.gz", + "bismark/methylation_calls/methylation_calls/CpG_OT_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz", + "bismark/methylation_calls/methylation_calls/CpG_OT_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz", + "bismark/methylation_calls/methylation_calls/CpG_OT_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz", + "bismark/methylation_calls/methylation_coverage", + "bismark/methylation_calls/methylation_coverage/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz", + "bismark/methylation_calls/methylation_coverage/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bismark.cov.gz", + "bismark/methylation_calls/methylation_coverage/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bismark.cov.gz", + "bismark/methylation_calls/methylation_coverage/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bismark.cov.gz", + "bismark/methylation_calls/splitting_report", + "bismark/methylation_calls/splitting_report/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt", + "bismark/methylation_calls/splitting_report/SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt", + "bismark/methylation_calls/splitting_report/SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt", + "bismark/methylation_calls/splitting_report/SRR389222_sub3_trimmed_bismark_bt2.deduplicated_splitting_report.txt", + "bismark/reports", + "bismark/reports/Ecoli_10K_methylated_1_val_1_bismark_bt2_PE_report.html", + "bismark/reports/SRR389222_sub1_trimmed_bismark_bt2_SE_report.html", + "bismark/reports/SRR389222_sub2_trimmed_bismark_bt2_SE_report.html", + "bismark/reports/SRR389222_sub3_trimmed_bismark_bt2_SE_report.html", + "bismark/summary", + "bismark/summary/bismark_summary_report.html", + "bismark/summary/bismark_summary_report.txt", + "fastqc", + "fastqc/Ecoli_10K_methylated_1_fastqc.html", + "fastqc/Ecoli_10K_methylated_2_fastqc.html", + "fastqc/SRR389222_sub1_fastqc.html", + "fastqc/SRR389222_sub2_fastqc.html", + "fastqc/SRR389222_sub3_fastqc.html", + "fastqc/zips", + "fastqc/zips/Ecoli_10K_methylated_1_fastqc.zip", + "fastqc/zips/Ecoli_10K_methylated_2_fastqc.zip", + "fastqc/zips/SRR389222_sub1_fastqc.zip", + "fastqc/zips/SRR389222_sub2_fastqc.zip", + "fastqc/zips/SRR389222_sub3_fastqc.zip", + "multiqc", + "multiqc/bismark", + "multiqc/bismark/multiqc_data", + "multiqc/bismark/multiqc_data/bismark-methylation-dp.txt", + "multiqc/bismark/multiqc_data/bismark_alignment.txt", + "multiqc/bismark/multiqc_data/bismark_deduplication.txt", + "multiqc/bismark/multiqc_data/bismark_mbias_CHG_R1.txt", + "multiqc/bismark/multiqc_data/bismark_mbias_CHG_R2.txt", + "multiqc/bismark/multiqc_data/bismark_mbias_CHH_R1.txt", + "multiqc/bismark/multiqc_data/bismark_mbias_CHH_R2.txt", + "multiqc/bismark/multiqc_data/bismark_mbias_CpG_R1.txt", + 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"nextflow": "24.04.4" + }, + "timestamp": "2024-10-21T17:43:14.505236122" + } +} \ No newline at end of file diff --git a/tests/bismark_hisat.nf.test b/tests/bismark_hisat.nf.test new file mode 100644 index 00000000..8ac37b1e --- /dev/null +++ b/tests/bismark_hisat.nf.test @@ -0,0 +1,60 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "../main.nf" + config "./nextflow.config" + + test("Params: bismark_hisat") { + when { + params { + aligner = "bismark_hisat" + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name + stable_name, + // All files with stable contents + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + ).match() } + ) + } + } + + test("Params: bismark_hisat with hisat2-index") { + when { + params { + aligner = "bismark_hisat" + bismark_index = "https://github.com/nf-core/test-datasets/raw/methylseq/reference/Hisat2_Index.tar.gz" + outdir = "$outputDir" + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size() + ).match() } + ) + } + } + +} diff --git a/tests/bismark_hisat.nf.test.snap b/tests/bismark_hisat.nf.test.snap new file mode 100644 index 00000000..0e92c1eb --- /dev/null +++ b/tests/bismark_hisat.nf.test.snap @@ -0,0 +1,591 @@ +{ + "Params: bismark_hisat with hisat2-index": { + "content": [ + 43 + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.2" + }, + "timestamp": "2024-10-12T07:21:45.007688275" + }, + "Params: bismark_hisat": { + "content": [ + 43, + { + "BISMARK_ALIGN": { + "bismark": "0.24.2" + }, + "BISMARK_GENOMEPREPARATION": { + "bismark": "0.24.2" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "QUALIMAP_BAMQC": { + "qualimap": 2.3 + }, + "TRIMGALORE": { + "trimgalore": "0.6.10", + "cutadapt": 4.2 + }, + "Workflow": { + "nf-core/methylseq": "v2.7.0" + } + }, + [ + "bismark_hisat", + "bismark_hisat/alignments", + "bismark_hisat/alignments/logs", + "bismark_hisat/alignments/logs/Ecoli_10K_methylated_1_val_1_bismark_hisat2_PE_report.txt", + 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100644 index 00000000..b8715634 --- /dev/null +++ b/tests/bismark_hisat_rrbs.nf.test @@ -0,0 +1,41 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "../main.nf" + config "./nextflow.config" + + test("Params: bismark_hisat | rrbs") { + when { + params { + aligner = "bismark_hisat" + rrbs = true + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name + stable_name, + // All files with stable contents + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + ).match() } + ) + } + } + +} diff --git a/tests/bismark_hisat_rrbs.nf.test.snap b/tests/bismark_hisat_rrbs.nf.test.snap new file mode 100644 index 00000000..0eb368cc --- /dev/null +++ b/tests/bismark_hisat_rrbs.nf.test.snap @@ -0,0 +1,584 @@ +{ + "Params: bismark_hisat | rrbs": { + "content": [ + 39, + { + "BISMARK_ALIGN": { + "bismark": "0.24.2" + }, + "BISMARK_GENOMEPREPARATION": { + "bismark": "0.24.2" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "QUALIMAP_BAMQC": { + "qualimap": 2.3 + }, + "TRIMGALORE": { + "trimgalore": "0.6.10", + "cutadapt": 4.2 + }, + "Workflow": { + "nf-core/methylseq": "v2.7.0" 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"SRR389222_sub3.deduplicated.sorted.bam", + "99246979468cb998c02b26b5c8ac4ee4" + ] + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-21T17:48:05.852952347" + } +} \ No newline at end of file diff --git a/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test b/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test new file mode 100644 index 00000000..2f2b0a0c --- /dev/null +++ b/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test @@ -0,0 +1,42 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "../main.nf" + config "./nextflow.config" + + test("Params: bismark_hisat | save_reference | save_align_intermeds") { + when { + params { + aligner = "bismark_hisat" + save_reference = true + save_align_intermeds = true + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name + stable_name, + // All files with stable contents + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + ).match() } + ) + } + } + +} diff --git a/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test.snap 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"qualimap_coverage_histogram.txt:md5,b78964924f4985d97f6dff7ced688d29", + "qualimap_gc_content.txt:md5,ad345dd40fe367f2138776c8ea2b257f", + "qualimap_genome_fraction.txt:md5,9a1c3d3f7349cf1c2af1c5878dac4185", + "qualimap_insert_size.txt:md5,8327f805cbaf1c61ca3128b6c16c7dfd", + "genome_results.txt:md5,9b6cc47e6ecfa1a9bd03b79f9ab764e6", + "genome_results.txt:md5,e808a20446012ad2643385cf316605c0", + "genome_results.txt:md5,41833cb9a1cfb8945c0fd6711981e58e", + "genome_results.txt:md5,10636e2fb7eb1ac2cf246483405ae973" + ], + [ + [ + "Ecoli_10K_methylated.sorted.bam", + "a1bd6455ebe3ecb43fe55e02d149d98" + ], + [ + "Ecoli_10K_methylated_1_val_1_bismark_hisat2_pe.bam", + "534293d598c34366bcde057d3972b60" + ], + [ + "SRR389222_sub1.sorted.bam", + "b203a3936158c51706e56c3a4e16191e" + ], + [ + "SRR389222_sub1_trimmed_bismark_hisat2.bam", + "4ee84a71b73e58161226cc4d8ca1f9b9" + ], + [ + "SRR389222_sub2.sorted.bam", + "6f8b0d6f085cc6a3d597b8839ba94b8b" + ], + [ + "SRR389222_sub2_trimmed_bismark_hisat2.bam", + "3e3ccc351ed92abdced1edb24fbb94ed" + ], + [ + "SRR389222_sub3.sorted.bam", + "c03e8e797936ca18a7e286977c7cf16" + ], + [ + "SRR389222_sub3_trimmed_bismark_hisat2.bam", + "74c99f560772eb303bd4bc257f3a8898" + ], + [ + "Ecoli_10K_methylated.deduplicated.sorted.bam", + "a1bd6455ebe3ecb43fe55e02d149d98" + ], + [ + "SRR389222_sub1.deduplicated.sorted.bam", + "8d735d1f6337b2cf2fa720773ce34b60" + ], + [ + "SRR389222_sub2.deduplicated.sorted.bam", + "45d53a598b4e59d173e32ea1f0558083" + ], + [ + "SRR389222_sub3.deduplicated.sorted.bam", + "ddb15c5ef0686837616d73f45c154b8d" + ] + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-21T17:49:33.437253199" + } +} \ No newline at end of file diff --git a/tests/bismark_nomeseq.nf.test b/tests/bismark_nomeseq.nf.test new file mode 100644 index 00000000..4cd98ef6 --- /dev/null +++ b/tests/bismark_nomeseq.nf.test @@ -0,0 +1,40 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "../main.nf" + config "./nextflow.config" + + test("Params: bismark | nomeseq") { + when { + params { + nomeseq = true + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name + stable_name, + // All files with stable contents + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + ).match() } + ) + } + } + +} diff --git a/tests/bismark_nomeseq.nf.test.snap b/tests/bismark_nomeseq.nf.test.snap new file mode 100644 index 00000000..d23aa5fe --- /dev/null +++ b/tests/bismark_nomeseq.nf.test.snap @@ -0,0 +1,625 @@ +{ + "Params: bismark | nomeseq": { + "content": [ + 47, + { + "BISMARK_ALIGN": { + "bismark": "0.24.2" + }, + "BISMARK_GENOMEPREPARATION": { + "bismark": "0.24.2" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "QUALIMAP_BAMQC": { + "qualimap": 2.3 + }, + "TRIMGALORE": { + "trimgalore": "0.6.10", + "cutadapt": 4.2 + }, + "Workflow": { + "nf-core/methylseq": "v2.7.0" + } + }, + [ + "bismark", + "bismark/alignments", + "bismark/alignments/logs", + "bismark/alignments/logs/Ecoli_10K_methylated_1_val_1_bismark_bt2_PE_report.txt", + "bismark/alignments/logs/SRR389222_sub1_trimmed_bismark_bt2_SE_report.txt", + "bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt", + "bismark/alignments/logs/SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt", + "bismark/coverage2cytosine", + "bismark/coverage2cytosine/coverage", + "bismark/coverage2cytosine/coverage/Ecoli_10K_methylated.NOMe.CpG.cov.gz", + "bismark/coverage2cytosine/coverage/Ecoli_10K_methylated.NOMe.GpC.cov.gz", + "bismark/coverage2cytosine/coverage/SRR389222_sub1.NOMe.CpG.cov.gz", + "bismark/coverage2cytosine/coverage/SRR389222_sub1.NOMe.GpC.cov.gz", + "bismark/coverage2cytosine/coverage/SRR389222_sub2.NOMe.CpG.cov.gz", + "bismark/coverage2cytosine/coverage/SRR389222_sub2.NOMe.GpC.cov.gz", + "bismark/coverage2cytosine/coverage/SRR389222_sub3.NOMe.CpG.cov.gz", + "bismark/coverage2cytosine/coverage/SRR389222_sub3.NOMe.GpC.cov.gz", + "bismark/coverage2cytosine/reports", + "bismark/coverage2cytosine/reports/Ecoli_10K_methylated.NOMe.CpG_report.txt.gz", + "bismark/coverage2cytosine/reports/Ecoli_10K_methylated.NOMe.GpC_report.txt.gz", + "bismark/coverage2cytosine/reports/SRR389222_sub1.NOMe.CpG_report.txt.gz", + "bismark/coverage2cytosine/reports/SRR389222_sub1.NOMe.GpC_report.txt.gz", + "bismark/coverage2cytosine/reports/SRR389222_sub2.NOMe.CpG_report.txt.gz", + "bismark/coverage2cytosine/reports/SRR389222_sub2.NOMe.GpC_report.txt.gz", + "bismark/coverage2cytosine/reports/SRR389222_sub3.NOMe.CpG_report.txt.gz", + "bismark/coverage2cytosine/reports/SRR389222_sub3.NOMe.GpC_report.txt.gz", + "bismark/coverage2cytosine/summaries", + "bismark/coverage2cytosine/summaries/Ecoli_10K_methylated.cytosine_context_summary.txt", + "bismark/coverage2cytosine/summaries/SRR389222_sub1.cytosine_context_summary.txt", + "bismark/coverage2cytosine/summaries/SRR389222_sub2.cytosine_context_summary.txt", + 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"SRR389222_sub1.deduplicated.sorted.bam", + "3f11ef5fbbda3797fd6217728e4f00d3" + ], + [ + "SRR389222_sub2.deduplicated.sorted.bam", + "b01f29fc1d8d46922a69df09c636b4c4" + ], + [ + "SRR389222_sub3.deduplicated.sorted.bam", + "347195c04c9ffd2a2b10967a6682fc69" + ] + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-21T17:50:56.499718354" + } +} \ No newline at end of file diff --git a/tests/bismark_rrbs.nf.test b/tests/bismark_rrbs.nf.test new file mode 100644 index 00000000..185a9998 --- /dev/null +++ b/tests/bismark_rrbs.nf.test @@ -0,0 +1,40 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "../main.nf" + config "./nextflow.config" + + test("Params: bismark | rrbs") { + when { + params { + rrbs = true + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name + stable_name, + // All files with stable contents + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + ).match() } + ) + } + } + +} diff --git a/tests/bismark_rrbs.nf.test.snap b/tests/bismark_rrbs.nf.test.snap new file mode 100644 index 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"SRR389222_sub1_trimmed_bismark_bt2.bam", + "2cfcb459e44dc624e3807632f118e659" + ], + [ + "SRR389222_sub2_trimmed_bismark_bt2.bam", + "bc7acb48fa6b4c8cdf1ced034af8e2c" + ], + [ + "SRR389222_sub3_trimmed_bismark_bt2.bam", + "7c02cfebfd9ee3360050142e2d144a20" + ], + [ + "Ecoli_10K_methylated.deduplicated.sorted.bam", + "38e388c7f8db48f3e06d16d2611faafe" + ], + [ + "SRR389222_sub1.deduplicated.sorted.bam", + "d042804716ccaa1f8061a309e8d79467" + ], + [ + "SRR389222_sub2.deduplicated.sorted.bam", + "a55f63182990117bc57714cb8227a57e" + ], + [ + "SRR389222_sub3.deduplicated.sorted.bam", + "605fc4a383cc488c53b66c6b5494eba" + ] + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-21T17:52:32.475797707" + } +} \ No newline at end of file diff --git a/tests/bismark_save_reference_save_align_intermeds.nf.test b/tests/bismark_save_reference_save_align_intermeds.nf.test new file mode 100644 index 00000000..cc5fc7a0 --- /dev/null +++ b/tests/bismark_save_reference_save_align_intermeds.nf.test @@ -0,0 +1,42 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "../main.nf" + config "./nextflow.config" + + test("Params: bismark | save_reference | save_align_intermeds") { + when { + params { + aligner = "bismark" + save_reference = true + save_align_intermeds = true + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name + stable_name, + // All files with stable contents + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + ).match() } + ) + } + } + +} diff --git a/tests/bismark_save_reference_save_align_intermeds.nf.test.snap b/tests/bismark_save_reference_save_align_intermeds.nf.test.snap new file mode 100644 index 00000000..8ec9d79e --- /dev/null +++ b/tests/bismark_save_reference_save_align_intermeds.nf.test.snap @@ -0,0 +1,654 @@ +{ + "Params: bismark | save_reference | save_align_intermeds": { + "content": [ + 43, + { + "BISMARK_ALIGN": { + "bismark": "0.24.2" + }, + "BISMARK_GENOMEPREPARATION": { + "bismark": "0.24.2" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "QUALIMAP_BAMQC": { + "qualimap": 2.3 + }, + "TRIMGALORE": { + "trimgalore": "0.6.10", + "cutadapt": 4.2 + }, + "Workflow": { + "nf-core/methylseq": "v2.7.0" + } + }, + [ + "bismark", + "bismark/alignments", + "bismark/alignments/Ecoli_10K_methylated.sorted.bam", + "bismark/alignments/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.bam", + "bismark/alignments/SRR389222_sub1.sorted.bam", + "bismark/alignments/SRR389222_sub1_trimmed_bismark_bt2.bam", + "bismark/alignments/SRR389222_sub2.sorted.bam", + "bismark/alignments/SRR389222_sub2_trimmed_bismark_bt2.bam", + "bismark/alignments/SRR389222_sub3.sorted.bam", + "bismark/alignments/SRR389222_sub3_trimmed_bismark_bt2.bam", + "bismark/alignments/logs", + "bismark/alignments/logs/Ecoli_10K_methylated_1_val_1_bismark_bt2_PE_report.txt", + "bismark/alignments/logs/SRR389222_sub1_trimmed_bismark_bt2_SE_report.txt", + "bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt", + "bismark/alignments/logs/SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt", 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], + [ + "SRR389222_sub2.sorted.bam", + "d347232a4fc5b1e02e98254b6ce97ae6" + ], + [ + "SRR389222_sub2_trimmed_bismark_bt2.bam", + "a94aeadc2acebd0a46647bb95acf2d55" + ], + [ + "SRR389222_sub3.sorted.bam", + "29648af285a183ae2194790b5a325186" + ], + [ + "SRR389222_sub3_trimmed_bismark_bt2.bam", + "6579ca7e49b9d7760ea5b3f3456739a1" + ], + [ + "Ecoli_10K_methylated.deduplicated.sorted.bam", + "a54ab7c96f9523a4ccd25fd69f6905f8" + ], + [ + "SRR389222_sub1.deduplicated.sorted.bam", + "3f11ef5fbbda3797fd6217728e4f00d3" + ], + [ + "SRR389222_sub2.deduplicated.sorted.bam", + "b01f29fc1d8d46922a69df09c636b4c4" + ], + [ + "SRR389222_sub3.deduplicated.sorted.bam", + "347195c04c9ffd2a2b10967a6682fc69" + ] + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-21T18:10:42.065837136" + } +} \ No newline at end of file diff --git a/tests/bismark_skip_deduplication.nf.test b/tests/bismark_skip_deduplication.nf.test new file mode 100644 index 00000000..055b77e6 --- /dev/null +++ b/tests/bismark_skip_deduplication.nf.test @@ -0,0 +1,40 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "../main.nf" + config "./nextflow.config" + + test("Params: bismark | skip_deduplication") { + when { + params { + skip_deduplication = true + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name + stable_name, + // All files with stable contents + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + ).match() } + ) + } + } + +} diff --git a/tests/bismark_skip_deduplication.nf.test.snap b/tests/bismark_skip_deduplication.nf.test.snap new file mode 100644 index 00000000..13bf50eb --- /dev/null +++ b/tests/bismark_skip_deduplication.nf.test.snap @@ -0,0 +1,586 @@ +{ + "Params: bismark | skip_deduplication": { + "content": [ + 39, + { + "BISMARK_ALIGN": { + "bismark": "0.24.2" + }, + "BISMARK_GENOMEPREPARATION": { + "bismark": "0.24.2" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "QUALIMAP_BAMQC": { + "qualimap": 2.3 + }, + "TRIMGALORE": { + "trimgalore": "0.6.10", + "cutadapt": 4.2 + }, + "Workflow": { + "nf-core/methylseq": "v2.7.0" + 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"SRR389222_sub1_trimmed_bismark_bt2.bam", + "934288bfc59d40ff7e73706d07815fb" + ], + [ + "SRR389222_sub2_trimmed_bismark_bt2.bam", + "a94aeadc2acebd0a46647bb95acf2d55" + ], + [ + "SRR389222_sub3_trimmed_bismark_bt2.bam", + "6579ca7e49b9d7760ea5b3f3456739a1" + ], + [ + "Ecoli_10K_methylated.deduplicated.sorted.bam", + "a54ab7c96f9523a4ccd25fd69f6905f8" + ], + [ + "SRR389222_sub1.deduplicated.sorted.bam", + "fa0f34c0d0d4d321b89973f23e033aa1" + ], + [ + "SRR389222_sub2.deduplicated.sorted.bam", + "d347232a4fc5b1e02e98254b6ce97ae6" + ], + [ + "SRR389222_sub3.deduplicated.sorted.bam", + "29648af285a183ae2194790b5a325186" + ] + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-21T17:54:28.816433456" + } +} \ No newline at end of file diff --git a/tests/bismark_skip_multiqc.nf.test b/tests/bismark_skip_multiqc.nf.test new file mode 100644 index 00000000..99cbe91f --- /dev/null +++ b/tests/bismark_skip_multiqc.nf.test @@ -0,0 +1,40 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "../main.nf" + config "./nextflow.config" + + test("Params: bismark | skip_multiqc") { + when { + params { + skip_multiqc = true + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name + stable_name, + // All files with stable contents + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + ).match() } + ) + } + } + +} diff --git a/tests/bismark_skip_multiqc.nf.test.snap b/tests/bismark_skip_multiqc.nf.test.snap new file mode 100644 index 00000000..84d72c00 --- /dev/null +++ b/tests/bismark_skip_multiqc.nf.test.snap @@ -0,0 +1,581 @@ +{ + "Params: bismark | skip_multiqc": { + "content": [ + 43, + { + "BISMARK_ALIGN": { + "bismark": "0.24.2" + }, + "BISMARK_GENOMEPREPARATION": { + "bismark": "0.24.2" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "QUALIMAP_BAMQC": { + "qualimap": 2.3 + }, + "TRIMGALORE": { + "trimgalore": "0.6.10", + "cutadapt": 4.2 + }, + "Workflow": { + "nf-core/methylseq": "v2.7.0" + } + }, + [ + "bismark", + "bismark/alignments", + "bismark/alignments/logs", + 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+ ], + [ + "SRR389222_sub3.deduplicated.sorted.bam", + "347195c04c9ffd2a2b10967a6682fc69" + ] + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-21T17:55:48.550138313" + } +} \ No newline at end of file diff --git a/tests/bismark_skip_trimming.nf.test b/tests/bismark_skip_trimming.nf.test new file mode 100644 index 00000000..28b415c6 --- /dev/null +++ b/tests/bismark_skip_trimming.nf.test @@ -0,0 +1,40 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "../main.nf" + config "./nextflow.config" + + test("Params: bismark | skip_trimming") { + when { + params { + skip_trimming = true + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name + stable_name, + // All files with stable contents + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + ).match() } + ) + } + } + +} diff --git a/tests/bismark_skip_trimming.nf.test.snap b/tests/bismark_skip_trimming.nf.test.snap new file mode 100644 index 00000000..97e616c6 --- /dev/null +++ b/tests/bismark_skip_trimming.nf.test.snap @@ -0,0 +1,538 @@ +{ + "Params: bismark 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"SRR389222_sub3_bismark_bt2.deduplicated_splitting_report.txt:md5,c015374e9b11c9eb7cb1359cb437f7be", + "bismark-methylation-dp.txt:md5,475ce6b3c6f53158847d554ef22993db", + "bismark_alignment.txt:md5,7d00ed2e752ebf0ee7baedc206c6572b", + "bismark_deduplication.txt:md5,e319d929f7d2e163bafba0a48dda554e", + "bismark_mbias_CHG_R1.txt:md5,56716bd5e0f29c8dca3963d2e8111bb8", + "bismark_mbias_CHG_R2.txt:md5,5ad75a070d97528e6285b9501c5bba78", + "bismark_mbias_CHH_R1.txt:md5,9e10b7c831ea33d4a726250fa02a610b", + "bismark_mbias_CHH_R2.txt:md5,8b9b1fad299392ce2014201d1f6a49a1", + "bismark_mbias_CpG_R1.txt:md5,541deb88c74b1700c53b6c4232a39a88", + "bismark_mbias_CpG_R2.txt:md5,6305c6b3a6aa994e620d97af0d7bdf4c", + "bismark_strand_alignment.txt:md5,c298d65a4fb50d87ad7f419d0211e7a3", + "fastqc-status-check-heatmap.txt:md5,218c2a7efbb9c02f652fa78fc739c866", + "fastqc_adapter_content_plot.txt:md5,48d8bd5ece984a74972ce0a0e814dd07", + "fastqc_overrepresented_sequences_plot.txt:md5,9c4b7064950b5b2c486d556984f21e9e", + "fastqc_per_base_n_content_plot.txt:md5,019d5cd4f61a31f4e7016140ca8ee36e", + "fastqc_per_base_sequence_quality_plot.txt:md5,e4c7d522114eab9bc9101e7ee9d83c8f", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,302659bee8a02b6a38b24fe25f8eaa87", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,c75b396eb5dda8682fb1652a9b2e92a3", + "fastqc_per_sequence_quality_scores_plot.txt:md5,548c593f4a8be2d8627fc3bd1c280611", + "fastqc_sequence_counts_plot.txt:md5,58eeeb06bc9dcc1764c7daf0847d6bbf", + "fastqc_sequence_duplication_levels_plot.txt:md5,9e5712db9aa39b5754ea1e0c49cfff15", + "fastqc_top_overrepresented_sequences_table.txt:md5,6dfc5334a09c05392ea17369aa742d01", + "multiqc_bismark_alignment.txt:md5,005c0d22d94af339b7145207dd64d92e", + "multiqc_bismark_dedup.txt:md5,363c336840edee5ba1d2f40ce85aa2b6", + "multiqc_bismark_methextract.txt:md5,8c74286850870be34285f1b8a96ab641", + "multiqc_citations.txt:md5,3a8f645306d124626931e2eb6ade3dfc", + "qualimap_coverage_histogram.txt:md5,937adee56f45d795a2dc79d4eeb6704d", + "qualimap_gc_content.txt:md5,d1c2209fd60ab1ef987dcdcbf11ace26", + "qualimap_genome_fraction.txt:md5,e9d696b5fb6e7a660e69b378039907a5", + "qualimap_insert_size.txt:md5,8327f805cbaf1c61ca3128b6c16c7dfd", + "genome_results.txt:md5,024419d0c463732287b0edf27647e21a", + "genome_results.txt:md5,445e1cd701e53837e7747383264f0b15", + "genome_results.txt:md5,cb7e3c8a8097ffd58fc9d4b0f293cf64", + "genome_results.txt:md5,56b2c5bc4772ef6439af3a3b8c97cfaa" + ], + [ + [ + "Ecoli_10K_methylated.deduplicated.sorted.bam", + "b49754b06cf7a7fc8d31b973e5ee9cc3" + ], + [ + "SRR389222_sub1.deduplicated.sorted.bam", + "35d55bee1ca653931716e40dac4aba30" + ], + [ + "SRR389222_sub2.deduplicated.sorted.bam", + "563d9803a88c3ccc7c97b09cb7c7757c" + ], + [ + "SRR389222_sub3.deduplicated.sorted.bam", + "6d92c014b65f85fbdfa1abeca8a5f47f" + ] + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-17T11:09:41.623493366" + } +} \ No newline at end of file diff --git a/tests/bwameth.nf.test b/tests/bwameth.nf.test new file mode 100644 index 00000000..04283574 --- /dev/null +++ b/tests/bwameth.nf.test @@ -0,0 +1,60 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "../main.nf" + config "./nextflow.config" + + test("Params: bwameth") { + when { + params { + aligner = "bwameth" + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name + stable_name, + // All files with stable contents + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + ).match() } + ) + } + } + + test("Params: bwameth with bwameth-index") { + when { + params { + aligner = "bwameth" + bwameth_index = "https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bwameth_Index.tar.gz" + outdir = "$outputDir" + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size() + ).match() } + ) + } + } + +} diff --git a/tests/bwameth.nf.test.snap b/tests/bwameth.nf.test.snap new file mode 100644 index 00000000..6ce8c6d3 --- /dev/null +++ b/tests/bwameth.nf.test.snap @@ -0,0 +1,453 @@ +{ + "Params: bwameth": { + "content": [ + 50, + { + "BWAMETH_ALIGN": { + "bwameth": "0.2.7" + }, + "BWAMETH_INDEX": { + "bwameth": "0.2.7" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "QUALIMAP_BAMQC": { + "qualimap": 2.3 + }, + "TRIMGALORE": { + "trimgalore": "0.6.10", + "cutadapt": 4.2 + }, + "Workflow": { + "nf-core/methylseq": "v2.7.0" + } + }, + [ + "bwameth", + "bwameth/alignments", + "bwameth/alignments/samtools_stats", + "bwameth/alignments/samtools_stats/Ecoli_10K_methylated.flagstat", + "bwameth/alignments/samtools_stats/Ecoli_10K_methylated.stats", + "bwameth/alignments/samtools_stats/SRR389222_sub1.flagstat", + "bwameth/alignments/samtools_stats/SRR389222_sub1.stats", + "bwameth/alignments/samtools_stats/SRR389222_sub2.flagstat", + "bwameth/alignments/samtools_stats/SRR389222_sub2.stats", + "bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat", + "bwameth/alignments/samtools_stats/SRR389222_sub3.stats", + "bwameth/deduplicated", + "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam", + "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam.bai", + "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam", + "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam.bai", + "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam", + "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam.bai", + "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam", + "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam.bai", + "bwameth/deduplicated/picard_metrics", + "bwameth/deduplicated/picard_metrics/Ecoli_10K_methylated.markdup.sorted.MarkDuplicates.metrics.txt", + "bwameth/deduplicated/picard_metrics/SRR389222_sub1.markdup.sorted.MarkDuplicates.metrics.txt", + "bwameth/deduplicated/picard_metrics/SRR389222_sub2.markdup.sorted.MarkDuplicates.metrics.txt", + "bwameth/deduplicated/picard_metrics/SRR389222_sub3.markdup.sorted.MarkDuplicates.metrics.txt", + "fastqc", + "fastqc/Ecoli_10K_methylated_1_fastqc.html", + "fastqc/Ecoli_10K_methylated_2_fastqc.html", + "fastqc/SRR389222_sub1_fastqc.html", + "fastqc/SRR389222_sub2_fastqc.html", + "fastqc/SRR389222_sub3_fastqc.html", + "fastqc/zips", + "fastqc/zips/Ecoli_10K_methylated_1_fastqc.zip", + "fastqc/zips/Ecoli_10K_methylated_2_fastqc.zip", + "fastqc/zips/SRR389222_sub1_fastqc.zip", + "fastqc/zips/SRR389222_sub2_fastqc.zip", + "fastqc/zips/SRR389222_sub3_fastqc.zip", + "methyldackel", + "methyldackel/Ecoli_10K_methylated.markdup.sorted_CpG.bedGraph", + "methyldackel/SRR389222_sub1.markdup.sorted_CpG.bedGraph", + "methyldackel/SRR389222_sub2.markdup.sorted_CpG.bedGraph", + "methyldackel/SRR389222_sub3.markdup.sorted_CpG.bedGraph", + "methyldackel/mbias", + "methyldackel/mbias/Ecoli_10K_methylated.mbias.txt", + "methyldackel/mbias/SRR389222_sub1.mbias.txt", + "methyldackel/mbias/SRR389222_sub2.mbias.txt", + "methyldackel/mbias/SRR389222_sub3.mbias.txt", + "multiqc", + "multiqc/bwameth", + "multiqc/bwameth/multiqc_data", + "multiqc/bwameth/multiqc_data/cutadapt_filtered_reads_plot.txt", + "multiqc/bwameth/multiqc_data/cutadapt_trimmed_sequences_plot_3_Counts.txt", + "multiqc/bwameth/multiqc_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", + "multiqc/bwameth/multiqc_data/fastqc-status-check-heatmap.txt", + "multiqc/bwameth/multiqc_data/fastqc_adapter_content_plot.txt", + "multiqc/bwameth/multiqc_data/fastqc_overrepresented_sequences_plot.txt", + "multiqc/bwameth/multiqc_data/fastqc_per_base_n_content_plot.txt", + "multiqc/bwameth/multiqc_data/fastqc_per_base_sequence_quality_plot.txt", + "multiqc/bwameth/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt", + "multiqc/bwameth/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/bwameth/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt", + "multiqc/bwameth/multiqc_data/fastqc_sequence_counts_plot.txt", + "multiqc/bwameth/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/bwameth/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/bwameth/multiqc_data/multiqc.log", + "multiqc/bwameth/multiqc_data/multiqc_citations.txt", + "multiqc/bwameth/multiqc_data/multiqc_cutadapt.txt", + "multiqc/bwameth/multiqc_data/multiqc_data.json", + "multiqc/bwameth/multiqc_data/multiqc_fastqc.txt", + "multiqc/bwameth/multiqc_data/multiqc_general_stats.txt", + "multiqc/bwameth/multiqc_data/multiqc_picard_dups.txt", + "multiqc/bwameth/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt", + "multiqc/bwameth/multiqc_data/multiqc_samtools_flagstat.txt", + "multiqc/bwameth/multiqc_data/multiqc_samtools_stats.txt", + "multiqc/bwameth/multiqc_data/multiqc_software_versions.txt", + "multiqc/bwameth/multiqc_data/multiqc_sources.txt", + "multiqc/bwameth/multiqc_data/picard_deduplication.txt", + 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"2024-10-12T07:40:41.336750081" + } +} \ No newline at end of file diff --git a/tests/bwameth_rrbs.nf.test b/tests/bwameth_rrbs.nf.test new file mode 100644 index 00000000..cc0fba43 --- /dev/null +++ b/tests/bwameth_rrbs.nf.test @@ -0,0 +1,41 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "../main.nf" + config "./nextflow.config" + + test("Params: bwameth | rrbs") { + when { + params { + aligner = "bwameth" + rrbs = true + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name + stable_name, + // All files with stable contents + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + ).match() } + ) + } + } + +} diff --git a/tests/bwameth_rrbs.nf.test.snap b/tests/bwameth_rrbs.nf.test.snap new file mode 100644 index 00000000..59f497d9 --- /dev/null +++ b/tests/bwameth_rrbs.nf.test.snap @@ -0,0 +1,398 @@ +{ + "Params: bwameth | rrbs": { + "content": [ + 42, + { + "BWAMETH_ALIGN": { + "bwameth": "0.2.7" + }, + "BWAMETH_INDEX": { + "bwameth": "0.2.7" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "QUALIMAP_BAMQC": { + "qualimap": 2.3 + }, + "TRIMGALORE": { + 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a/tests/bwameth_save_reference_save_align_intermeds.nf.test b/tests/bwameth_save_reference_save_align_intermeds.nf.test new file mode 100644 index 00000000..2ce41cd3 --- /dev/null +++ b/tests/bwameth_save_reference_save_align_intermeds.nf.test @@ -0,0 +1,42 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "../main.nf" + config "./nextflow.config" + + test("Params: bwameth | save_reference | save_align_intermeds") { + when { + params { + aligner = "bwameth" + save_reference = true + save_align_intermeds = true + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name + stable_name, + // All files with stable contents + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + ).match() } + ) + } + } + +} diff --git a/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap b/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap new file mode 100644 index 00000000..546c1371 --- /dev/null +++ b/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap @@ -0,0 +1,501 @@ +{ + "Params: bwameth | save_reference | save_align_intermeds": { + "content": [ + 50, + { + "BWAMETH_ALIGN": { + "bwameth": "0.2.7" + }, + "BWAMETH_INDEX": { + "bwameth": "0.2.7" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "QUALIMAP_BAMQC": { + "qualimap": 2.3 + }, + "TRIMGALORE": { + "trimgalore": "0.6.10", + "cutadapt": 4.2 + }, + "Workflow": { + "nf-core/methylseq": "v2.7.0" + } + }, + [ + "bwameth", + "bwameth/alignments", + "bwameth/alignments/Ecoli_10K_methylated.bam", + "bwameth/alignments/Ecoli_10K_methylated.sorted.bam", + "bwameth/alignments/Ecoli_10K_methylated.sorted.bam.bai", + "bwameth/alignments/SRR389222_sub1.bam", + "bwameth/alignments/SRR389222_sub1.sorted.bam", + "bwameth/alignments/SRR389222_sub1.sorted.bam.bai", + "bwameth/alignments/SRR389222_sub2.bam", + "bwameth/alignments/SRR389222_sub2.sorted.bam", + "bwameth/alignments/SRR389222_sub2.sorted.bam.bai", + "bwameth/alignments/SRR389222_sub3.bam", + "bwameth/alignments/SRR389222_sub3.sorted.bam", + "bwameth/alignments/SRR389222_sub3.sorted.bam.bai", + "bwameth/alignments/samtools_stats", + "bwameth/alignments/samtools_stats/Ecoli_10K_methylated.flagstat", + "bwameth/alignments/samtools_stats/Ecoli_10K_methylated.stats", + "bwameth/alignments/samtools_stats/SRR389222_sub1.flagstat", + "bwameth/alignments/samtools_stats/SRR389222_sub1.stats", + "bwameth/alignments/samtools_stats/SRR389222_sub2.flagstat", + "bwameth/alignments/samtools_stats/SRR389222_sub2.stats", + "bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat", + "bwameth/alignments/samtools_stats/SRR389222_sub3.stats", + "bwameth/deduplicated", + "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam", + "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam.bai", + "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam", + "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam.bai", + "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam", + "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam.bai", + "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam", + "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam.bai", + "bwameth/deduplicated/picard_metrics", + "bwameth/deduplicated/picard_metrics/Ecoli_10K_methylated.markdup.sorted.MarkDuplicates.metrics.txt", + "bwameth/deduplicated/picard_metrics/SRR389222_sub1.markdup.sorted.MarkDuplicates.metrics.txt", + "bwameth/deduplicated/picard_metrics/SRR389222_sub2.markdup.sorted.MarkDuplicates.metrics.txt", + "bwameth/deduplicated/picard_metrics/SRR389222_sub3.markdup.sorted.MarkDuplicates.metrics.txt", + "bwameth/reference_genome", + "bwameth/reference_genome/BwamethIndex", + "bwameth/reference_genome/BwamethIndex/genome.fa.bwameth.c2t", + "bwameth/reference_genome/BwamethIndex/genome.fa.bwameth.c2t.amb", + "bwameth/reference_genome/BwamethIndex/genome.fa.bwameth.c2t.ann", + "bwameth/reference_genome/BwamethIndex/genome.fa.bwameth.c2t.bwt", + "bwameth/reference_genome/BwamethIndex/genome.fa.bwameth.c2t.pac", + "bwameth/reference_genome/BwamethIndex/genome.fa.bwameth.c2t.sa", + "fastqc", + "fastqc/Ecoli_10K_methylated_1_fastqc.html", + "fastqc/Ecoli_10K_methylated_2_fastqc.html", + "fastqc/SRR389222_sub1_fastqc.html", + "fastqc/SRR389222_sub2_fastqc.html", + "fastqc/SRR389222_sub3_fastqc.html", + "fastqc/zips", + "fastqc/zips/Ecoli_10K_methylated_1_fastqc.zip", + "fastqc/zips/Ecoli_10K_methylated_2_fastqc.zip", + "fastqc/zips/SRR389222_sub1_fastqc.zip", + "fastqc/zips/SRR389222_sub2_fastqc.zip", + "fastqc/zips/SRR389222_sub3_fastqc.zip", + "methyldackel", + "methyldackel/Ecoli_10K_methylated.markdup.sorted_CpG.bedGraph", + "methyldackel/SRR389222_sub1.markdup.sorted_CpG.bedGraph", + "methyldackel/SRR389222_sub2.markdup.sorted_CpG.bedGraph", + "methyldackel/SRR389222_sub3.markdup.sorted_CpG.bedGraph", + "methyldackel/mbias", + "methyldackel/mbias/Ecoli_10K_methylated.mbias.txt", + "methyldackel/mbias/SRR389222_sub1.mbias.txt", + "methyldackel/mbias/SRR389222_sub2.mbias.txt", + 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00000000..0b208bf4 --- /dev/null +++ b/tests/bwameth_skip_deduplication.nf.test @@ -0,0 +1,41 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "../main.nf" + config "./nextflow.config" + + test("Params: bwameth | skip_deduplication") { + when { + params { + aligner = "bwameth" + skip_deduplication = true + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name + stable_name, + // All files with stable contents + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + ).match() } + ) + } + } + +} diff --git a/tests/bwameth_skip_deduplication.nf.test.snap b/tests/bwameth_skip_deduplication.nf.test.snap new file mode 100644 index 00000000..f73c18ae --- /dev/null +++ b/tests/bwameth_skip_deduplication.nf.test.snap @@ -0,0 +1,398 @@ +{ + "Params: bwameth | skip_deduplication": { + "content": [ + 42, + { + "BWAMETH_ALIGN": { + "bwameth": "0.2.7" + }, + "BWAMETH_INDEX": { + "bwameth": "0.2.7" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "QUALIMAP_BAMQC": { + "qualimap": 2.3 + }, + "TRIMGALORE": { + "trimgalore": "0.6.10", + "cutadapt": 4.2 + }, + "Workflow": { + 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a/tests/bwameth_skip_trimming.nf.test b/tests/bwameth_skip_trimming.nf.test new file mode 100644 index 00000000..3b01599d --- /dev/null +++ b/tests/bwameth_skip_trimming.nf.test @@ -0,0 +1,41 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "../main.nf" + config "./nextflow.config" + + test("Params: bwameth | skip_trimming") { + when { + params { + aligner = "bwameth" + skip_trimming = true + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number 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a/tests/default.nf.test b/tests/default.nf.test new file mode 100644 index 00000000..6a210a07 --- /dev/null +++ b/tests/default.nf.test @@ -0,0 +1,58 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "../main.nf" + config "./nextflow.config" + + test("Params: default") { + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name + stable_name, + // All files with stable contents + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + ).match() } + ) + } + } + + test("Params: default with bowtie2-index") { + when { + params { + bismark_index = "https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bowtie2_Index.tar.gz" + outdir = "$outputDir" + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size() + ).match() } + ) + } + } + +} diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap new file mode 100644 index 00000000..675f4e67 --- /dev/null +++ b/tests/default.nf.test.snap @@ -0,0 +1,591 @@ +{ + "Params: default with bowtie2-index": { 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"CHH_OB_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz:md5,9469ac28e4369032b855ce1a794a56a4", + "CHH_OB_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz:md5,3c48fa14cc07ca041a35efd978ef877a", + "CHH_OB_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz:md5,68b5405d8de91c7046ab46fc5c42ee30", + "CHH_OT_Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,112a5d2beba2f8ebda273ca3bec98d88", + "CHH_OT_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz:md5,aa6ed81df517be3a61e787dea65282a9", + "CHH_OT_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz:md5,3ecf0ca20803514bc823e449d392f274", + "CHH_OT_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz:md5,7ed9df0d59ee786d06bf291efcdd3a48", + "CpG_OB_Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,bbe0a5f137b8768036aced610d17c666", + "CpG_OB_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz:md5,f0404fc1fc18c7ff58e8766b405239ed", + "CpG_OB_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz:md5,2f0dd539df6b5943496158ccb62edc7b", + "CpG_OB_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz:md5,0bd78a1708fb8126af553c94ab8c8371", + "CpG_OT_Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,8bb4cb59815cc9e260dcfa332fcb5ae9", + "CpG_OT_SRR389222_sub1_trimmed_bismark_bt2.deduplicated.txt.gz:md5,d031ae437256c87d12ed9d9049c30c9a", + "CpG_OT_SRR389222_sub2_trimmed_bismark_bt2.deduplicated.txt.gz:md5,5a6e4dfe3e90164ecf8ef6c7917ed9f2", + "CpG_OT_SRR389222_sub3_trimmed_bismark_bt2.deduplicated.txt.gz:md5,984aea9c77f8171f0e0a86d5289a180b", + "Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,8e6ba6fe66416d73e7f94b4da9ca77b1", + "SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,5377d9fff4f1bf5b98dc2310fbeb6ec9", + "SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,4713bda7b4f2bb16ce23853aea763cbd", + "SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,f9a07c3e11e0caad6df3cd2e4d94d8ac", + "Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt:md5,f41a6752f220b1cf567ac04e71fb730a", + "SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,94f18ee855566ef9842b4909e3d3dd88", + "SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,7c3526e022e97e49677f7428badef420", + "SRR389222_sub3_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,e8d2bf21731b6ed517c56385061b1dee", + "bismark-methylation-dp.txt:md5,dcbe642c42e31d8e480a2e46b97bbd45", + "bismark_alignment.txt:md5,544a74ea0f32005b0c886af79a6fad5b", + "bismark_deduplication.txt:md5,db387240d46c09b0b952ed8b54855e76", + "bismark_mbias_CHG_R1.txt:md5,1a2a02f5f48e312a7cfa91ec253c1f49", + "bismark_mbias_CHG_R2.txt:md5,1f6523b48bda086d29f70265187e7475", + "bismark_mbias_CHH_R1.txt:md5,bcd25ac0c71b5ec120e948bc165f54d4", + "bismark_mbias_CHH_R2.txt:md5,5e32a8b39118c3592b088a0b69ae1f21", + "bismark_mbias_CpG_R1.txt:md5,0da9724e4a303148c39b6f4c18b8876b", + "bismark_mbias_CpG_R2.txt:md5,46cca816038163d0f629fed7ada212b8", + "bismark_strand_alignment.txt:md5,a8738f981bab911b95ffe9d3434f2b08", + "cutadapt_filtered_reads_plot.txt:md5,ff1b6d4011a5be5410b9404f7ff56c56", + "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,57d07c19b0c30dc88df96c30bedcdc33", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,1e5ca4193f8290c5c812334d03615b41", + "fastqc-status-check-heatmap.txt:md5,218c2a7efbb9c02f652fa78fc739c866", + "fastqc_adapter_content_plot.txt:md5,48d8bd5ece984a74972ce0a0e814dd07", + "fastqc_overrepresented_sequences_plot.txt:md5,9c4b7064950b5b2c486d556984f21e9e", + "fastqc_per_base_n_content_plot.txt:md5,019d5cd4f61a31f4e7016140ca8ee36e", + "fastqc_per_base_sequence_quality_plot.txt:md5,e4c7d522114eab9bc9101e7ee9d83c8f", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,302659bee8a02b6a38b24fe25f8eaa87", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,c75b396eb5dda8682fb1652a9b2e92a3", + "fastqc_per_sequence_quality_scores_plot.txt:md5,548c593f4a8be2d8627fc3bd1c280611", + "fastqc_sequence_counts_plot.txt:md5,58eeeb06bc9dcc1764c7daf0847d6bbf", + "fastqc_sequence_duplication_levels_plot.txt:md5,9e5712db9aa39b5754ea1e0c49cfff15", + "fastqc_top_overrepresented_sequences_table.txt:md5,6dfc5334a09c05392ea17369aa742d01", + "multiqc_bismark_alignment.txt:md5,40ab86041f508d3f1a63bde20cab5440", + "multiqc_bismark_dedup.txt:md5,d09a5de4d81a3207efb6a8937d060e46", + "multiqc_bismark_methextract.txt:md5,825f57cdf45203406e583beb495afccc", + "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", + "multiqc_cutadapt.txt:md5,f7a61369244b1e040d264e6913b8a839", + "qualimap_coverage_histogram.txt:md5,7cd194077fe839edf034b44cc73dd024", + "qualimap_gc_content.txt:md5,4f6ec70d9fb71ffe5f2f99f44fe5ef0c", + "qualimap_genome_fraction.txt:md5,3e528946a376ae752b57adaaa73f5cdf", + "qualimap_insert_size.txt:md5,8327f805cbaf1c61ca3128b6c16c7dfd", + "genome_results.txt:md5,e2a57140a56e0e4a1905c70084ccbb41", + "genome_results.txt:md5,69a3dc8568127c50b0decb29757230ee", + "genome_results.txt:md5,13d933d61649b837de72a418d5126c1b", + "genome_results.txt:md5,235830239cfc43d8e84c049b1e9b180a" + ], + [ + [ + "Ecoli_10K_methylated.deduplicated.sorted.bam", + "a54ab7c96f9523a4ccd25fd69f6905f8" + ], + [ + "SRR389222_sub1.deduplicated.sorted.bam", + "3f11ef5fbbda3797fd6217728e4f00d3" + ], + [ + "SRR389222_sub2.deduplicated.sorted.bam", + "b01f29fc1d8d46922a69df09c636b4c4" + ], + [ + "SRR389222_sub3.deduplicated.sorted.bam", + "347195c04c9ffd2a2b10967a6682fc69" + ] + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-21T18:05:06.16706255" + } +} \ No newline at end of file diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy deleted file mode 100644 index 311403cc..00000000 --- a/tests/lib/UTILS.groovy +++ /dev/null @@ -1,11 +0,0 @@ -// Function to remove Nextflow version from software_versions.yml - -class UTILS { - public static String removeNextflowVersion(outputDir) { - def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml - if (softwareVersions.containsKey("Workflow")) { - softwareVersions.Workflow.remove("Nextflow") - } - return softwareVersions - } -} diff --git a/tests/nextflow.config b/tests/nextflow.config new file mode 100644 index 00000000..794a5cb8 --- /dev/null +++ b/tests/nextflow.config @@ -0,0 +1,42 @@ +/* +======================================================================================== + Nextflow config file for running tests +======================================================================================== +*/ + +params { + // Base directory for nf-core/modules test data + modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/' + // Base directory for nf-core/methylseq test data + pipelines_testdata_base_path = 'https://github.com/nf-core/test-datasets/raw/methylseq/' + + // Input data + input = "${projectDir}/assets/samplesheet.csv" + fasta = "${params.pipelines_testdata_base_path}/reference/genome.fa" + fasta_index = "${params.pipelines_testdata_base_path}/reference/genome.fa.fai" + outdir = 'results' +} + +// Impose sensible resource limits for testing +process { + withName: '.*' { + cpus = 2 + memory = 3.GB + time = 2.h + } + + withName: PRESEQ_LCEXTRAP { + errorStrategy = 'ignore' + } +} + +// Impose same minimum Nextflow version as the pipeline for testing +manifest { + nextflowVersion = '!>=24.04.2' +} + +// Disable all Nextflow reporting options +timeline { enabled = false } +report { enabled = false } +trace { enabled = false } +dag { enabled = false } diff --git a/tests/pipeline/bismark/main.nf.test b/tests/pipeline/bismark/main.nf.test deleted file mode 100644 index 11483301..00000000 --- a/tests/pipeline/bismark/main.nf.test +++ /dev/null @@ -1,224 +0,0 @@ -nextflow_pipeline { - - name "Test Workflow main.nf" - script "main.nf" - - tag "bismark" - tag "pipeline" - - test("Bismark Single-End") { - when { - params { - aligner = "bismark" - save_reference = true - outdir = "$outputDir" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(path("$outputDir/bismark/deduplicated/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bam"), - path("$outputDir/bismark/deduplicated/SRR389222_trimmed_bismark_bt2.deduplicated.bam"), - path("$outputDir/bismark/methylation_calls/bedGraph/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/mbias/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/mbias/SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_calls/").list(), - path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), - path("$outputDir/bismark/reference_genome/BismarkIndex/").list(), - path("$outputDir/qualimap/Ecoli/genome_results.txt"), - path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end") }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_software_versions") }, - { assert new File("$outputDir/bismark/alignments/logs/Ecoli_1_val_1_bismark_bt2_PE_report.txt").exists() }, - { assert new File("$outputDir/bismark/alignments/logs/SRR389222_trimmed_bismark_bt2_SE_report.txt").exists() }, - { assert new File("$outputDir/bismark/reports/Ecoli_1_val_1_bismark_bt2_PE_report.html").exists() }, - { assert new File("$outputDir/bismark/reports/SRR389222_trimmed_bismark_bt2_SE_report.html").exists() }, - { assert new File("$outputDir/bismark/summary/bismark_summary_report.html").exists() }, - { assert new File("$outputDir/bismark/summary/bismark_summary_report.txt").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, - { assert new File("$outputDir/multiqc/bismark/multiqc_report.html").exists() }, - { assert new File("$outputDir/trimgalore/logs/Ecoli_1.fastq.gz_trimming_report.txt").exists() }, - { assert new File("$outputDir/trimgalore/logs/Ecoli_2.fastq.gz_trimming_report.txt").exists() }, - { assert new File("$outputDir/trimgalore/logs/SRR389222.fastq.gz_trimming_report.txt").exists() } - ) - } - } - - test("Bismark Single-End With Index") { - when { - params { - aligner = "bismark" - bismark_index = "https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bowtie2_Index.tar.gz" - cytosine_report = true - outdir = "$outputDir" - } - } - - then { - assertAll( - { assert workflow.success }, - ) - } - } - - test("Bismark Single-End With RRBS") { - when { - params { - aligner = "bismark" - skip_trimming = true - save_reference = true - rrbs = true - outdir = "$outputDir" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(path("$outputDir/bismark/alignments/Ecoli_10K_methylated_R1_bismark_bt2_pe.bam"), - path("$outputDir/bismark/alignments/SRR389222.merged_bismark_bt2.bam"), - path("$outputDir/bismark/methylation_calls/bedGraph/Ecoli_10K_methylated_R1_bismark_bt2_pe.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222.merged_bismark_bt2.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/mbias/Ecoli_10K_methylated_R1_bismark_bt2_pe.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/mbias/SRR389222.merged_bismark_bt2.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/Ecoli_10K_methylated_R1_bismark_bt2_pe.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222.merged_bismark_bt2.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_calls/").list(), - path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_10K_methylated_R1_bismark_bt2_pe_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222.merged_bismark_bt2_splitting_report.txt"), - path("$outputDir/bismark/reference_genome/BismarkIndex/").list(), - path("$outputDir/qualimap/Ecoli/genome_results.txt"), - path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end_rrbs") }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_rrbs_software_versions") }, - { assert new File("$outputDir/bismark/alignments/logs/Ecoli_10K_methylated_R1_bismark_bt2_PE_report.txt").exists() }, - { assert new File("$outputDir/bismark/alignments/logs/SRR389222.merged_bismark_bt2_SE_report.txt").exists() }, - { assert new File("$outputDir/bismark/reports/Ecoli_10K_methylated_R1_bismark_bt2_PE_report.html").exists() }, - { assert new File("$outputDir/bismark/reports/SRR389222.merged_bismark_bt2_SE_report.html").exists() }, - { assert new File("$outputDir/bismark/summary/bismark_summary_report.html").exists() }, - { assert new File("$outputDir/bismark/summary/bismark_summary_report.txt").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, - { assert new File("$outputDir/multiqc/bismark/multiqc_report.html").exists() } - ) - } - } - - test("Bismark Single-End With RRBS With Index") { - when { - params { - aligner = "bismark" - skip_trimming = true - rrbs = true - bismark_index = "https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bowtie2_Index.tar.gz" - cytosine_report = true - outdir = "$outputDir" - } - } - - then { - assertAll( - { assert workflow.success }, - ) - } - } - - test("Bismark Single-End NOMe-seq") { - when { - params { - aligner = "bismark" - nomeseq = true - outdir = "$outputDir" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(path("$outputDir/bismark/coverage2cytosine/coverage/Ecoli.NOMe.CpG.cov.gz"), - path("$outputDir/bismark/coverage2cytosine/coverage/Ecoli.NOMe.GpC.cov.gz"), - path("$outputDir/bismark/coverage2cytosine/coverage/SRR389222.NOMe.CpG.cov.gz"), - path("$outputDir/bismark/coverage2cytosine/coverage/SRR389222.NOMe.GpC.cov.gz"), - path("$outputDir/bismark/deduplicated/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bam"), - path("$outputDir/bismark/deduplicated/SRR389222_trimmed_bismark_bt2.deduplicated.bam"), - path("$outputDir/bismark/methylation_calls/bedGraph/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/mbias/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/mbias/SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_calls/").list(), - path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), - path("$outputDir/cat/SRR389222.merged.fastq.gz"), - path("$outputDir/qualimap/Ecoli/genome_results.txt"), - path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end_nomeseq") }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_nomeseq_software_versions") }, - { assert new File("$outputDir/bismark/alignments/logs/Ecoli_1_val_1_bismark_bt2_PE_report.txt").exists() }, - { assert new File("$outputDir/bismark/alignments/logs/SRR389222_trimmed_bismark_bt2_SE_report.txt").exists() }, - { assert new File("$outputDir/bismark/reports/Ecoli_1_val_1_bismark_bt2_PE_report.html").exists() }, - { assert new File("$outputDir/bismark/reports/SRR389222_trimmed_bismark_bt2_SE_report.html").exists() }, - { assert new File("$outputDir/bismark/summary/bismark_summary_report.html").exists() }, - { assert new File("$outputDir/bismark/summary/bismark_summary_report.txt").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, - { assert new File("$outputDir/multiqc/bismark/multiqc_report.html").exists() }, - { assert new File("$outputDir/trimgalore/logs/Ecoli_1.fastq.gz_trimming_report.txt").exists() }, - { assert new File("$outputDir/trimgalore/logs/Ecoli_2.fastq.gz_trimming_report.txt").exists() }, - { assert new File("$outputDir/trimgalore/logs/SRR389222.fastq.gz_trimming_report.txt").exists() } - ) - } - } - - test("Bismark Clip R1 - 2") { - when { - params { - aligner = "bismark" - em_seq = true - clip_r1 = 2 - outdir = "$outputDir" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(path("$outputDir/bismark/deduplicated/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bam"), - path("$outputDir/bismark/deduplicated/SRR389222_trimmed_bismark_bt2.deduplicated.bam"), - path("$outputDir/bismark/methylation_calls/bedGraph/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), - path("$outputDir/bismark/methylation_calls/mbias/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/mbias/SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark/methylation_calls/methylation_calls/").list(), - path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), - path("$outputDir/cat/SRR389222.merged.fastq.gz"), - path("$outputDir/qualimap/Ecoli/genome_results.txt"), - path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("clip_r1") }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("clip_r1_software_versions") }, - { assert new File("$outputDir/bismark/alignments/logs/Ecoli_1_val_1_bismark_bt2_PE_report.txt").exists() }, - { assert new File("$outputDir/bismark/alignments/logs/SRR389222_trimmed_bismark_bt2_SE_report.txt").exists() }, - { assert new File("$outputDir/bismark/reports/Ecoli_1_val_1_bismark_bt2_PE_report.html").exists() }, - { assert new File("$outputDir/bismark/reports/SRR389222_trimmed_bismark_bt2_SE_report.html").exists() }, - { assert new File("$outputDir/bismark/summary/bismark_summary_report.html").exists() }, - { assert new File("$outputDir/bismark/summary/bismark_summary_report.txt").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, - { assert new File("$outputDir/multiqc/bismark/multiqc_report.html").exists() }, - { assert new File("$outputDir/trimgalore/logs/Ecoli_1.fastq.gz_trimming_report.txt").exists() }, - { assert new File("$outputDir/trimgalore/logs/Ecoli_2.fastq.gz_trimming_report.txt").exists() }, - { assert new File("$outputDir/trimgalore/logs/SRR389222.fastq.gz_trimming_report.txt").exists() } - ) - } - } -} diff --git a/tests/pipeline/bismark/main.nf.test.snap b/tests/pipeline/bismark/main.nf.test.snap deleted file mode 100644 index 281ff290..00000000 --- a/tests/pipeline/bismark/main.nf.test.snap +++ /dev/null @@ -1,202 +0,0 @@ -{ - "single_end_software_versions": { - "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0}}" - ], - "timestamp": "2024-01-05T13:33:44.592961646" - }, - "single_end_nomeseq_software_versions": { - "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0}}" - ], - "timestamp": "2024-01-05T13:38:45.868954182" - }, - "single_end_rrbs_software_versions": { - "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.6.0}}" - ], - "timestamp": "2024-01-05T13:36:19.58008405" - }, - "single_end_nomeseq": { - "content": [ - "Ecoli.NOMe.CpG.cov.gz:md5,c2c4db8d0a2ec32d572e75b01b2f7d81", - "Ecoli.NOMe.GpC.cov.gz:md5,a2b56291dbe8b344ee03a3ae58de8807", - "SRR389222.NOMe.CpG.cov.gz:md5,9738cb2fd47a65851626fc48d264c1b4", - "SRR389222.NOMe.GpC.cov.gz:md5,d5e6d60c93e76c7476b132b6aa4f8395", - "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bam:md5,caa027599dac71c50c24de1857dbf5c7", - "SRR389222_trimmed_bismark_bt2.deduplicated.bam:md5,7dba45955ae74159596a6ab41a9dcc87", - "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,88e599178b08907aab7d248302b7d37e", - "SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,fe6b3655db6da21bdd3076947e062f0b", - "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt:md5,29f3b882a51b63ce77d3d9c69b0e5f85", - "SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,bc48b8895f9ce84205a25899cf551624", - "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,962fe67f41f5e03d8e321ed381369513", - "SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,82a55b84888ad5fe530f97c348738fdb", - [ - "CHG_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,9c2248d95d96d6c315c65f1b8dc3bc39", - "CHG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,9d8098ce1a27c23961e20b6a95f237d1", - "CHG_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,5e5aefaa3f63e73f30342ad843eb210b", - "CHG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,e68463946c5bfdf461c3aa81524f8837", - "CHH_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,65f2afc6b1c76209af1acd1d4277a1cc", - "CHH_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,6834286d8d07a1b3a4399f71b5b3c3f8", - "CHH_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,978ad87fef01e39283a620253320ee45", - "CHH_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,4347c873d1a7c772a448dd01351e5c0f", - "CpG_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,54def6bf13e27f38adbbd3dd06297596", - "CpG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,4dae933bcdc8c7d1de2f5e7239c1ae55", - "CpG_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,9712eef973883f44dcc0a307af28ba70", - "CpG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,49ec41948052a2a4a952f651df13b344" - ], - "Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt:md5,b759f31785293e8d952f1dd3246f9a7b", - "SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,1c4a4288b3bcf1bbaa6b99e3c4b53ce9", - "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", - "genome_results.txt:md5,886ffc763d05a84ead7f80a1d1db1fa2", - "genome_results.txt:md5,b99d4cfd82d21ac09ccb72865f9b3960" - ], - "timestamp": "2023-12-22T22:56:01.615992857" - }, - "clip_r1_software_versions": { - "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0}}" - ], - "timestamp": "2024-01-05T13:39:54.162519593" - }, - "single_end": { - "content": [ - "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bam:md5,caa027599dac71c50c24de1857dbf5c7", - "SRR389222_trimmed_bismark_bt2.deduplicated.bam:md5,7dba45955ae74159596a6ab41a9dcc87", - "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,58c9ba98d0638c26a30233b006a81172", - "SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,3a19363a47169044a01f7195eb83266c", - "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt:md5,29f3b882a51b63ce77d3d9c69b0e5f85", - "SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,bc48b8895f9ce84205a25899cf551624", - "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,8e6ba6fe66416d73e7f94b4da9ca77b1", - "SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,389dc4fee59e34967d9af49958cb5cbe", - [ - "CHG_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,9c2248d95d96d6c315c65f1b8dc3bc39", - "CHG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,9d8098ce1a27c23961e20b6a95f237d1", - "CHG_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,5e5aefaa3f63e73f30342ad843eb210b", - "CHG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,e68463946c5bfdf461c3aa81524f8837", - "CHH_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,65f2afc6b1c76209af1acd1d4277a1cc", - "CHH_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,6834286d8d07a1b3a4399f71b5b3c3f8", - "CHH_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,978ad87fef01e39283a620253320ee45", - "CHH_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,4347c873d1a7c772a448dd01351e5c0f", - "CpG_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,54def6bf13e27f38adbbd3dd06297596", - "CpG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,4dae933bcdc8c7d1de2f5e7239c1ae55", - "CpG_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,9712eef973883f44dcc0a307af28ba70", - "CpG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,49ec41948052a2a4a952f651df13b344" - ], - "Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt:md5,b759f31785293e8d952f1dd3246f9a7b", - "SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,1c4a4288b3bcf1bbaa6b99e3c4b53ce9", - [ - [ - [ - "BS_CT.1.bt2:md5,d53bef7d951c7d08e327944581c911eb", - "BS_CT.2.bt2:md5,752a03fc364115fc910e5a28ae154382", - "BS_CT.3.bt2:md5,b41e72eefad74e8ede411c78a5bd5dee", - "BS_CT.4.bt2:md5,02b3d1855a67fd9cbb4c411406a22fde", - "BS_CT.rev.1.bt2:md5,52ae603fff473b3b25eecd36c533edb9", - "BS_CT.rev.2.bt2:md5,0e290e05f7dae065cae54e29ed97afe5", - "genome_mfa.CT_conversion.fa:md5,4dd181b65f1f3549f4132c9a3759eee8" - ], - [ - "BS_GA.1.bt2:md5,9aff51b1712758b891b0c427a988977f", - "BS_GA.2.bt2:md5,579241d95941538b2e75bbdb6cfaa73d", - "BS_GA.3.bt2:md5,b41e72eefad74e8ede411c78a5bd5dee", - "BS_GA.4.bt2:md5,6b64fa496ffa2af2af235e1c87f06a25", - "BS_GA.rev.1.bt2:md5,dabf2d6f80ba7e8fc96dfdc203f6bbfd", - "BS_GA.rev.2.bt2:md5,fac2f8b39b0e15dec7aa79a0ecf12b49", - "genome_mfa.GA_conversion.fa:md5,3dee732bc344fd620c3a7322f52c6a5f" - ] - ], - "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de" - ], - "genome_results.txt:md5,886ffc763d05a84ead7f80a1d1db1fa2", - "genome_results.txt:md5,b99d4cfd82d21ac09ccb72865f9b3960" - ], - "timestamp": "2023-12-22T22:42:59.548979384" - }, - "single_end_rrbs": { - "content": [ - "Ecoli_10K_methylated_R1_bismark_bt2_pe.bam:md5,1497e3a06ee045cb82f834ddb4bcfe88", - "SRR389222.merged_bismark_bt2.bam:md5,c3e94ff13a934e0c78ebb6d40f7c8230", - "Ecoli_10K_methylated_R1_bismark_bt2_pe.bedGraph.gz:md5,58c9ba98d0638c26a30233b006a81172", - "SRR389222.merged_bismark_bt2.bedGraph.gz:md5,c154fe825d9bb867c9efcf55d6cb7e94", - "Ecoli_10K_methylated_R1_bismark_bt2_pe.M-bias.txt:md5,29f3b882a51b63ce77d3d9c69b0e5f85", - "SRR389222.merged_bismark_bt2.M-bias.txt:md5,514f544046333337f0f74b7386b8afa6", - "Ecoli_10K_methylated_R1_bismark_bt2_pe.bismark.cov.gz:md5,8e6ba6fe66416d73e7f94b4da9ca77b1", - "SRR389222.merged_bismark_bt2.bismark.cov.gz:md5,d4a5b741ca46b486bf165ede18baadd0", - [ - "CHG_OB_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,9c2248d95d96d6c315c65f1b8dc3bc39", - "CHG_OB_SRR389222.merged_bismark_bt2.txt.gz:md5,eeb08e87d7e3dca0acbb2c5ba2be66fb", - "CHG_OT_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,5e5aefaa3f63e73f30342ad843eb210b", - "CHG_OT_SRR389222.merged_bismark_bt2.txt.gz:md5,930f995efd5204b5b04a548afdef1a6e", - "CHH_OB_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,65f2afc6b1c76209af1acd1d4277a1cc", - "CHH_OB_SRR389222.merged_bismark_bt2.txt.gz:md5,a135c7e8a6c1b909a318ef17d47dca94", - "CHH_OT_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,978ad87fef01e39283a620253320ee45", - "CHH_OT_SRR389222.merged_bismark_bt2.txt.gz:md5,2a356ae7fe7774f140f11ed5d935f88c", - "CpG_OB_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,54def6bf13e27f38adbbd3dd06297596", - "CpG_OB_SRR389222.merged_bismark_bt2.txt.gz:md5,b8b2de10044869b6c1097afc21c878a0", - "CpG_OT_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,9712eef973883f44dcc0a307af28ba70", - "CpG_OT_SRR389222.merged_bismark_bt2.txt.gz:md5,9e517e44422a8bb22de1281ff2cd34d1" - ], - "Ecoli_10K_methylated_R1_bismark_bt2_pe_splitting_report.txt:md5,fa089f6146df9667862970b6ddc998b0", - "SRR389222.merged_bismark_bt2_splitting_report.txt:md5,0ece57f8fc3aa659d2f0b7a09cf48398", - [ - [ - [ - "BS_CT.1.bt2:md5,d53bef7d951c7d08e327944581c911eb", - "BS_CT.2.bt2:md5,752a03fc364115fc910e5a28ae154382", - "BS_CT.3.bt2:md5,b41e72eefad74e8ede411c78a5bd5dee", - "BS_CT.4.bt2:md5,02b3d1855a67fd9cbb4c411406a22fde", - "BS_CT.rev.1.bt2:md5,52ae603fff473b3b25eecd36c533edb9", - "BS_CT.rev.2.bt2:md5,0e290e05f7dae065cae54e29ed97afe5", - "genome_mfa.CT_conversion.fa:md5,4dd181b65f1f3549f4132c9a3759eee8" - ], - [ - "BS_GA.1.bt2:md5,9aff51b1712758b891b0c427a988977f", - "BS_GA.2.bt2:md5,579241d95941538b2e75bbdb6cfaa73d", - "BS_GA.3.bt2:md5,b41e72eefad74e8ede411c78a5bd5dee", - "BS_GA.4.bt2:md5,6b64fa496ffa2af2af235e1c87f06a25", - "BS_GA.rev.1.bt2:md5,dabf2d6f80ba7e8fc96dfdc203f6bbfd", - "BS_GA.rev.2.bt2:md5,fac2f8b39b0e15dec7aa79a0ecf12b49", - "genome_mfa.GA_conversion.fa:md5,3dee732bc344fd620c3a7322f52c6a5f" - ] - ], - "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de" - ], - "genome_results.txt:md5,97dc2b4df61a46ccd2714903186ecaf0", - "genome_results.txt:md5,f0d293867800a75becf2583c23729083" - ], - "timestamp": "2023-12-22T22:52:42.829793102" - }, - "clip_r1": { - "content": [ - "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bam:md5,b19bc9b84dd8d8000c05b04234689aca", - "SRR389222_trimmed_bismark_bt2.deduplicated.bam:md5,1bfe463dabf8727992e3ff6c19d8e7c1", - "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,e8b3933de21d7618cdaab650fe544b17", - "SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,bddc7c560a902b842b72e20a21274cba", - "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt:md5,83a004a3d957cf95f25933bcd828a8d4", - "SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,90a6b76d41112c6de391d3a017638d95", - "Ecoli_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,34aa02c199f1496df0704dd239373ebe", - "SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,03178f50ae4bf04a7b78d8bbdb8a77af", - [ - "CHG_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,3856b07ea51dea59b444a7483ca3db75", - "CHG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,e70e8a2ace2e602a967de256d299fb0d", - "CHG_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,c1ba1891636a6b99f4d1495b3ddf1a59", - "CHG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,f8867c4ee03fba6be823b7287cacfea3", - "CHH_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,4e9a0e61d47eefb64876431b3640ee95", - "CHH_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,32728cf447a470681f4e608008d514ae", - "CHH_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,10cd51608191667e027a9867dd84ab3f", - "CHH_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,2ec291cbfc4d64dbcd50603839129de1", - "CpG_OB_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,423aa4faf47d176a6b6cce134e1a9212", - "CpG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,873612f00ee6ef44e8bc0dcb9f4a35f6", - "CpG_OT_Ecoli_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,1e243313554fce1b06aba217c7123cae", - "CpG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,d86423a21b0d22188e188dc9f576135c" - ], - "Ecoli_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt:md5,db55b5dbf35e78de9c1c6b2f2ed1e45b", - "SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,9a1a5d1e6722dda9e8a1953a01c415d0", - "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", - "genome_results.txt:md5,2bbc428b0a5b9828df9fc4cd92806e12", - "genome_results.txt:md5,5631f1632df00985946641cfc1601633" - ], - "timestamp": "2023-12-22T22:57:38.05813974" - } -} \ No newline at end of file diff --git a/tests/pipeline/bismark_hisat/main.nf.test b/tests/pipeline/bismark_hisat/main.nf.test deleted file mode 100644 index 550fb843..00000000 --- a/tests/pipeline/bismark_hisat/main.nf.test +++ /dev/null @@ -1,132 +0,0 @@ -nextflow_pipeline { - - name "Test Workflow main.nf" - script "main.nf" - - tag "bismark_hisat" - tag "pipeline" - - test("Bismark Hisat Single-End") { - when { - params { - aligner = "bismark_hisat" - save_reference = true - outdir = "$outputDir" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(path("$outputDir/bismark_hisat/deduplicated/Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.bam"), - path("$outputDir/bismark_hisat/deduplicated/SRR389222_trimmed_bismark_hisat2.deduplicated.bam"), - path("$outputDir/bismark_hisat/methylation_calls/bedGraph/Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.bedGraph.gz"), - path("$outputDir/bismark_hisat/methylation_calls/bedGraph/SRR389222_trimmed_bismark_hisat2.deduplicated.bedGraph.gz"), - path("$outputDir/bismark_hisat/methylation_calls/mbias/Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.M-bias.txt"), - path("$outputDir/bismark_hisat/methylation_calls/mbias/SRR389222_trimmed_bismark_hisat2.deduplicated.M-bias.txt"), - path("$outputDir/bismark_hisat/methylation_calls/methylation_calls/").list(), - path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/SRR389222_trimmed_bismark_hisat2.deduplicated.bismark.cov.gz"), - path("$outputDir/bismark_hisat/methylation_calls/splitting_report/Ecoli_1_val_1_bismark_hisat2_pe.deduplicated_splitting_report.txt"), - path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222_trimmed_bismark_hisat2.deduplicated_splitting_report.txt"), - path("$outputDir/cat/SRR389222.merged.fastq.gz"), - path("$outputDir/qualimap/Ecoli/genome_results.txt"), - path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end") }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_software_versions") }, - { assert new File("$outputDir/bismark_hisat/alignments/logs/Ecoli_1_val_1_bismark_hisat2_PE_report.txt").exists() }, - { assert new File("$outputDir/bismark_hisat/alignments/logs/SRR389222_trimmed_bismark_hisat2_SE_report.txt").exists() }, - { assert new File("$outputDir/bismark_hisat/reports/Ecoli_1_val_1_bismark_hisat2_PE_report.html").exists() }, - { assert new File("$outputDir/bismark_hisat/reports/SRR389222_trimmed_bismark_hisat2_SE_report.html").exists() }, - { assert new File("$outputDir/bismark_hisat/summary/bismark_summary_report.html").exists() }, - { assert new File("$outputDir/bismark_hisat/summary/bismark_summary_report.txt").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, - { assert new File("$outputDir/multiqc/bismark_hisat/multiqc_report.html").exists() }, - { assert new File("$outputDir/trimgalore/logs/Ecoli_1.fastq.gz_trimming_report.txt").exists() }, - { assert new File("$outputDir/trimgalore/logs/Ecoli_2.fastq.gz_trimming_report.txt").exists() }, - { assert new File("$outputDir/trimgalore/logs/SRR389222.fastq.gz_trimming_report.txt").exists() } - ) - } - } - - test("Bismark Hisat Single-End With Index") { - when { - params { - aligner = "bismark_hisat" - bismark_index = "https://github.com/nf-core/test-datasets/raw/methylseq/reference/Hisat2_Index.tar.gz" - local_alignment = true - outdir = "$outputDir" - } - } - - then { - assertAll( - { assert workflow.success }, - ) - } - } - - test("Bismark Hisat Single-End With RRBS") { - when { - params { - aligner = "bismark_hisat" - save_reference = true - skip_trimming = true - rrbs = true - outdir = "$outputDir" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(path("$outputDir/bismark_hisat/alignments/Ecoli_10K_methylated_R1_bismark_hisat2_pe.bam"), - path("$outputDir/bismark_hisat/alignments/SRR389222.merged_bismark_hisat2.bam"), - path("$outputDir/bismark_hisat/methylation_calls/bedGraph/Ecoli_10K_methylated_R1_bismark_hisat2_pe.bedGraph.gz"), - path("$outputDir/bismark_hisat/methylation_calls/bedGraph/SRR389222.merged_bismark_hisat2.bedGraph.gz"), - path("$outputDir/bismark_hisat/methylation_calls/mbias/Ecoli_10K_methylated_R1_bismark_hisat2_pe.M-bias.txt"), - path("$outputDir/bismark_hisat/methylation_calls/mbias/SRR389222.merged_bismark_hisat2.M-bias.txt"), - path("$outputDir/bismark_hisat/methylation_calls/methylation_calls/").list(), - path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/Ecoli_10K_methylated_R1_bismark_hisat2_pe.bismark.cov.gz"), - path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/SRR389222.merged_bismark_hisat2.bismark.cov.gz"), - path("$outputDir/bismark_hisat/methylation_calls/splitting_report/Ecoli_10K_methylated_R1_bismark_hisat2_pe_splitting_report.txt"), - path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222.merged_bismark_hisat2_splitting_report.txt"), - path("$outputDir/cat/SRR389222.merged.fastq.gz"), - path("$outputDir/qualimap/Ecoli/genome_results.txt"), - path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end_rrbs") }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_rrbs_software_versions") }, - { assert new File("$outputDir/bismark_hisat/alignments/logs/Ecoli_10K_methylated_R1_bismark_hisat2_PE_report.txt").exists() }, - { assert new File("$outputDir/bismark_hisat/alignments/logs/SRR389222.merged_bismark_hisat2_SE_report.txt").exists() }, - { assert new File("$outputDir/bismark_hisat/reports/Ecoli_10K_methylated_R1_bismark_hisat2_PE_report.html").exists() }, - { assert new File("$outputDir/bismark_hisat/reports/SRR389222.merged_bismark_hisat2_SE_report.html").exists() }, - { assert new File("$outputDir/bismark_hisat/summary/bismark_summary_report.html").exists() }, - { assert new File("$outputDir/bismark_hisat/summary/bismark_summary_report.txt").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, - { assert new File("$outputDir/multiqc/bismark_hisat/multiqc_report.html").exists() } - ) - } - } - - test("Bismark Hisat Single-End With RRBS With Index") { - when { - params { - aligner = "bismark_hisat" - skip_trimming = true - rrbs = true - bismark_index = "https://github.com/nf-core/test-datasets/raw/methylseq/reference/Hisat2_Index.tar.gz" - local_alignment = true - outdir = "$outputDir" - } - } - - then { - assertAll( - { assert workflow.success }, - ) - } - } - -} diff --git a/tests/pipeline/bismark_hisat/main.nf.test.snap b/tests/pipeline/bismark_hisat/main.nf.test.snap deleted file mode 100644 index 07d914d9..00000000 --- a/tests/pipeline/bismark_hisat/main.nf.test.snap +++ /dev/null @@ -1,78 +0,0 @@ -{ - "single_end_software_versions": { - "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0}}" - ], - "timestamp": "2024-01-05T13:41:11.426077518" - }, - "single_end_rrbs_software_versions": { - "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.6.0}}" - ], - "timestamp": "2024-01-05T13:43:52.561148623" - }, - "single_end": { - "content": [ - "Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.bam:md5,ddfc84eb92f641020362f69e9e28a52d", - "SRR389222_trimmed_bismark_hisat2.deduplicated.bam:md5,aa60cf9dcf302c185b12ced6f302a06e", - "Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.bedGraph.gz:md5,357196071c54757566cdd0bb7ab79fa8", - "SRR389222_trimmed_bismark_hisat2.deduplicated.bedGraph.gz:md5,b20f17236ff64db1114343ff333a6d5b", - "Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.M-bias.txt:md5,5fd8655f4b9dba2249a52b769fe50faf", - "SRR389222_trimmed_bismark_hisat2.deduplicated.M-bias.txt:md5,b19356395d4ae1ad83bd3ec38276e580", - [ - "CHG_OB_Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,6d2ca2e6548640e3885c94a3ca6beae0", - "CHG_OB_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,9d8098ce1a27c23961e20b6a95f237d1", - "CHG_OT_Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,5e5aefaa3f63e73f30342ad843eb210b", - "CHG_OT_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,1180631ef093aade3a5195ce7ddfb3f6", - "CHH_OB_Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,abd48ddf1c9e844d8164de5150850d10", - "CHH_OB_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,6834286d8d07a1b3a4399f71b5b3c3f8", - "CHH_OT_Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,978ad87fef01e39283a620253320ee45", - "CHH_OT_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,c311a70c0c8b6a93c2055fcbec03a833", - "CpG_OB_Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,51f8b079b9fd91e23e495d9e0e289530", - "CpG_OB_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,4dae933bcdc8c7d1de2f5e7239c1ae55", - "CpG_OT_Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,9712eef973883f44dcc0a307af28ba70", - "CpG_OT_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,63e737eef999e2d6348e7ed2a7ce4402" - ], - "Ecoli_1_val_1_bismark_hisat2_pe.deduplicated.bismark.cov.gz:md5,d8342eca72089408d8e4d7c5ec5e95bf", - "SRR389222_trimmed_bismark_hisat2.deduplicated.bismark.cov.gz:md5,ad7a19cb9908844c47b7b871ff1223c2", - "Ecoli_1_val_1_bismark_hisat2_pe.deduplicated_splitting_report.txt:md5,bc2284d712455231a2dd772098ca8dd9", - "SRR389222_trimmed_bismark_hisat2.deduplicated_splitting_report.txt:md5,1f792e1fddb17140947f14008e1f9ffd", - "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", - "genome_results.txt:md5,3703ab8cc04a6f3307ea1ffcfe23479a", - "genome_results.txt:md5,7706d3790aee0e9244c490941ecd394f" - ], - "timestamp": "2023-12-22T22:14:39.589478621" - }, - "single_end_rrbs": { - "content": [ - "Ecoli_10K_methylated_R1_bismark_hisat2_pe.bam:md5,53c34edee0bc7f34c9f4e9a3685dd706", - "SRR389222.merged_bismark_hisat2.bam:md5,204123a5f7cd77cba3a90b904443c7eb", - "Ecoli_10K_methylated_R1_bismark_hisat2_pe.bedGraph.gz:md5,357196071c54757566cdd0bb7ab79fa8", - "SRR389222.merged_bismark_hisat2.bedGraph.gz:md5,d509b1e8e4ec03dcde48a127cf976594", - "Ecoli_10K_methylated_R1_bismark_hisat2_pe.M-bias.txt:md5,5fd8655f4b9dba2249a52b769fe50faf", - "SRR389222.merged_bismark_hisat2.M-bias.txt:md5,ea90b0495446d03e375aad42d598a9f9", - [ - "CHG_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,6d2ca2e6548640e3885c94a3ca6beae0", - "CHG_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,eeb08e87d7e3dca0acbb2c5ba2be66fb", - "CHG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,5e5aefaa3f63e73f30342ad843eb210b", - "CHG_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,7add3136b9f74de6aa83d38dde191060", - "CHH_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,abd48ddf1c9e844d8164de5150850d10", - "CHH_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,a135c7e8a6c1b909a318ef17d47dca94", - "CHH_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,978ad87fef01e39283a620253320ee45", - "CHH_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,8f1910f962b724592546a6187ad0a677", - "CpG_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,51f8b079b9fd91e23e495d9e0e289530", - "CpG_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,b8b2de10044869b6c1097afc21c878a0", - "CpG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,9712eef973883f44dcc0a307af28ba70", - "CpG_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,877b026664516cb8851c1d80bf0d8495" - ], - "Ecoli_10K_methylated_R1_bismark_hisat2_pe.bismark.cov.gz:md5,d8342eca72089408d8e4d7c5ec5e95bf", - "SRR389222.merged_bismark_hisat2.bismark.cov.gz:md5,29943eb00da6057a67e5530580668130", - "Ecoli_10K_methylated_R1_bismark_hisat2_pe_splitting_report.txt:md5,76868c2015864a3f7c2b4cd1738e4765", - "SRR389222.merged_bismark_hisat2_splitting_report.txt:md5,4a9e54ffb48c9bb1e5ac33aa77b25f5c", - "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", - "genome_results.txt:md5,58bf4e22f697120806f09b48d9ffdc9e", - "genome_results.txt:md5,ae5b10e9a3ffa1ac7a4f4e736228ec49" - ], - "timestamp": "2023-12-22T22:37:54.382841284" - } -} \ No newline at end of file diff --git a/tests/pipeline/bwameth/main.nf.test b/tests/pipeline/bwameth/main.nf.test deleted file mode 100644 index 1863371e..00000000 --- a/tests/pipeline/bwameth/main.nf.test +++ /dev/null @@ -1,123 +0,0 @@ -nextflow_pipeline { - - name "Test Workflow main.nf" - script "main.nf" - - tag "bwameth" - tag "pipeline" - - test("Bwameth Single-End") { - when { - params { - aligner = "bwameth" - save_reference = true - outdir = "$outputDir" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_software_versions") }, - { assert snapshot(path("$outputDir/bwameth/alignments/samtools_stats/Ecoli.flagstat"), - path("$outputDir/bwameth/alignments/samtools_stats/Ecoli.stats"), - path("$outputDir/bwameth/alignments/samtools_stats/SRR389222.flagstat"), - path("$outputDir/bwameth/alignments/samtools_stats/SRR389222.stats"), - path("$outputDir/bwameth/deduplicated/Ecoli.markdup.sorted.bam"), - path("$outputDir/bwameth/deduplicated/Ecoli.markdup.sorted.bam.bai"), - path("$outputDir/bwameth/deduplicated/SRR389222.markdup.sorted.bam"), - path("$outputDir/bwameth/deduplicated/SRR389222.markdup.sorted.bam.bai"), - path("$outputDir/bwameth/reference_genome/").list(), - path("$outputDir/cat/SRR389222.merged.fastq.gz"), - path("$outputDir/methyldackel/Ecoli.markdup.sorted_CpG.bedGraph"), - path("$outputDir/methyldackel/SRR389222.markdup.sorted_CpG.bedGraph"), - path("$outputDir/methyldackel/mbias/Ecoli.mbias.txt"), - path("$outputDir/methyldackel/mbias/SRR389222.mbias.txt"), - path("$outputDir/qualimap/Ecoli/genome_results.txt"), - path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end") }, - { assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, - { assert new File("$outputDir/multiqc/bwameth/multiqc_report.html").exists() }, - { assert new File("$outputDir/trimgalore/logs/Ecoli_1.fastq.gz_trimming_report.txt").exists() }, - { assert new File("$outputDir/trimgalore/logs/Ecoli_2.fastq.gz_trimming_report.txt").exists() }, - { assert new File("$outputDir/trimgalore/logs/SRR389222.fastq.gz_trimming_report.txt").exists() }, - { assert new File("$outputDir/bwameth/deduplicated/picard_metrics/Ecoli.markdup.sorted.MarkDuplicates.metrics.txt").exists() }, - { assert new File("$outputDir/bwameth/deduplicated/picard_metrics/SRR389222.markdup.sorted.MarkDuplicates.metrics.txt").exists() } - ) - } - } - - test("Bwameth Single-End With Index") { - when { - params { - aligner = "bwameth" - bwa_meth_index = "https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bwameth_Index.tar.gz" - methyl_kit = true - outdir = "$outputDir" - } - } - - then { - assertAll( - { assert workflow.success }, - ) - } - } - - test("Bwameth Single-End RRBS") { - when { - params { - aligner = "bwameth" - save_reference = true - skip_trimming = true - rrbs = true - save_reference = true - outdir = "$outputDir" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_rrbs_software_versions") }, - { assert snapshot(path("$outputDir/bwameth/alignments/samtools_stats/Ecoli.flagstat"), - path("$outputDir/bwameth/alignments/samtools_stats/Ecoli.stats"), - path("$outputDir/bwameth/alignments/samtools_stats/SRR389222.flagstat"), - path("$outputDir/bwameth/alignments/samtools_stats/SRR389222.stats"), - path("$outputDir/bwameth/reference_genome/").list(), - path("$outputDir/cat/SRR389222.merged.fastq.gz"), - path("$outputDir/methyldackel/Ecoli.sorted_CpG.bedGraph"), - path("$outputDir/methyldackel/SRR389222.sorted_CpG.bedGraph"), - path("$outputDir/methyldackel/mbias/Ecoli.mbias.txt"), - path("$outputDir/methyldackel/mbias/SRR389222.mbias.txt"), - path("$outputDir/qualimap/Ecoli/genome_results.txt"), - path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end_rrbs") }, - { assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() }, - { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, - { assert new File("$outputDir/multiqc/bwameth/multiqc_report.html").exists() } - ) - } - } - - test("Bwameth Single End RRBS With Index") { - when { - params { - aligner = "bwameth" - skip_trimming = true - rrbs = true - bwa_meth_index = "https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bwameth_Index.tar.gz" - methyl_kit = true - outdir = "$outputDir" - } - } - - then { - assertAll( - { assert workflow.success }, - ) - } - } - -} diff --git a/tests/pipeline/bwameth/main.nf.test.snap b/tests/pipeline/bwameth/main.nf.test.snap deleted file mode 100644 index fccd1fc2..00000000 --- a/tests/pipeline/bwameth/main.nf.test.snap +++ /dev/null @@ -1,72 +0,0 @@ -{ - "single_end_software_versions": { - "content": [ - "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.6.0}}" - ], - "timestamp": "2024-01-05T13:46:07.95961601" - }, - "single_end_rrbs_software_versions": { - "content": [ - "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.6.0}}" - ], - "timestamp": "2024-01-05T13:47:24.172597347" - }, - "single_end": { - "content": [ - "Ecoli.flagstat:md5,f520e87cc4050799a0dbed72909572ec", - "Ecoli.stats:md5,c09155913e0164da9010a0840618cf1f", - "SRR389222.flagstat:md5,f5a2dd6c9532bbfb8fe78aad010d8737", - "SRR389222.stats:md5,cc81b8c56d038e437a99d9c04b61ce2d", - "Ecoli.markdup.sorted.bam:md5,0d1c814b476521286a829dc64fc3490a", - "Ecoli.markdup.sorted.bam.bai:md5,befef6ce0a34e2ce7f66c073d9bf4abd", - "SRR389222.markdup.sorted.bam:md5,46b5b49280efe5d5c5d1692092e8926f", - "SRR389222.markdup.sorted.bam.bai:md5,ad6cfa0344e1ba5b9057ea39f337b3d2", - [ - [ - "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", - "genome.fa.bwameth.c2t:md5,e51d48ed28fa0c26e2f9c9f13d09403b", - "genome.fa.bwameth.c2t.amb:md5,010a242c6764efb30141868a45d698b3", - "genome.fa.bwameth.c2t.ann:md5,09b4db3d87a2d4dac9e10e807f377110", - "genome.fa.bwameth.c2t.bwt:md5,4646f8ae6bd523b7f4106bbd32eff95e", - "genome.fa.bwameth.c2t.pac:md5,a662d7add09698e25c8152fd2306ec66", - "genome.fa.bwameth.c2t.sa:md5,4a1e905b828396a1909669bc9c573d8d" - ] - ], - "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", - "Ecoli.markdup.sorted_CpG.bedGraph:md5,00132adede8128b3a111136713a2a4ff", - "SRR389222.markdup.sorted_CpG.bedGraph:md5,febd0f93f46dfccabf69dbba3f518add", - "Ecoli.mbias.txt:md5,3a448a2a6364b2de3129365a271c0534", - "SRR389222.mbias.txt:md5,fce04d733e066d0b933cedc602e2af81", - "genome_results.txt:md5,d1a1b49086982318f0f94ba7059f71a3", - "genome_results.txt:md5,c786cc367645cee286360707e2624dca" - ], - "timestamp": "2023-12-20T03:21:55.358959756" - }, - "single_end_rrbs": { - "content": [ - "Ecoli.flagstat:md5,7c3bae0f9c700dde88785a7e94c6ae2c", - "Ecoli.stats:md5,46eaf2559610c864bc4d27a08a0645b4", - "SRR389222.flagstat:md5,a90f1bdcb30f4d0597ccf69fe0b37b1f", - "SRR389222.stats:md5,b99800367e21a0c7c0d87e5fe29d9609", - [ - [ - "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", - "genome.fa.bwameth.c2t:md5,e51d48ed28fa0c26e2f9c9f13d09403b", - "genome.fa.bwameth.c2t.amb:md5,010a242c6764efb30141868a45d698b3", - "genome.fa.bwameth.c2t.ann:md5,09b4db3d87a2d4dac9e10e807f377110", - "genome.fa.bwameth.c2t.bwt:md5,4646f8ae6bd523b7f4106bbd32eff95e", - "genome.fa.bwameth.c2t.pac:md5,a662d7add09698e25c8152fd2306ec66", - "genome.fa.bwameth.c2t.sa:md5,4a1e905b828396a1909669bc9c573d8d" - ] - ], - "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", - "Ecoli.sorted_CpG.bedGraph:md5,41f4218573d5e4ff7016ffb42f13a551", - "SRR389222.sorted_CpG.bedGraph:md5,a754358e8b95db30602aa29835a896bd", - "Ecoli.mbias.txt:md5,ec13da6deba1ce147624bce065ec5df6", - "SRR389222.mbias.txt:md5,fce04d733e066d0b933cedc602e2af81", - "genome_results.txt:md5,cd545aa1ee209a1683374bfb5731ab0c", - "genome_results.txt:md5,199902f9d8f10f73bcb0a1ce29ceca5d" - ], - "timestamp": "2023-12-20T03:38:43.324010795" - } -} \ No newline at end of file diff --git a/workflows/methylseq.nf b/workflows/methylseq.nf deleted file mode 100644 index a351316e..00000000 --- a/workflows/methylseq.nf +++ /dev/null @@ -1,260 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - PRINT PARAMS SUMMARY -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -include { paramsSummaryLog; paramsSummaryMap; fromSamplesheet } from 'plugin/nf-validation' - -def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) -def citation = '\n' + WorkflowMain.citation(workflow) + '\n' -def summary_params = paramsSummaryMap(workflow) - -// Print parameter summary log to screen -log.info logo + paramsSummaryLog(workflow) + citation - -WorkflowMethylseq.initialise(params, log) - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CONFIG FILES -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) -ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty() -ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty() -ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - IMPORT LOCAL MODULES/SUBWORKFLOWS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -// -// SUBWORKFLOWS: Consisting of a mix of local and nf-core/modules -// -include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome' - -// Aligner: bismark or bismark_hisat -if( params.aligner =~ /bismark/ ){ - include { BISMARK } from '../subworkflows/local/bismark' -} -// Aligner: bwameth -else if ( params.aligner == 'bwameth' ){ - include { BWAMETH } from '../subworkflows/local/bwameth' -} - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - IMPORT NF-CORE MODULES/SUBWORKFLOWS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -// -// MODULE: Installed directly from nf-core/modules -// -include { CAT_FASTQ } from '../modules/nf-core/cat/fastq/main' -include { FASTQC } from '../modules/nf-core/fastqc/main' -include { MULTIQC } from '../modules/nf-core/multiqc/main' -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' -include { TRIMGALORE } from '../modules/nf-core/trimgalore/main' -include { QUALIMAP_BAMQC } from '../modules/nf-core/qualimap/bamqc/main' -include { PRESEQ_LCEXTRAP } from '../modules/nf-core/preseq/lcextrap/main' - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - RUN MAIN WORKFLOW -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -// Info required for completion email and summary -def multiqc_report = [] - -workflow METHYLSEQ { - - ch_versions = Channel.empty() - - // - // SUBWORKFLOW: Prepare any required reference genome indices - // - PREPARE_GENOME() - ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions) - - // - // Create input channel from input file provided through params.input - // - Channel - .fromSamplesheet("input") - .map { - meta, fastq_1, fastq_2 -> - if (!fastq_2) { - return [ meta + [ single_end:true ], [ fastq_1 ] ] - } else { - return [ meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] - } - } - .groupTuple() - .map { - meta, fastq -> - def meta_clone = meta.clone() - parts = meta_clone.id.split('_') - meta_clone.id = parts.length > 1 ? parts[0..-2].join('_') : meta_clone.id - [ meta_clone, fastq ] - } - .groupTuple(by: [0]) - .branch { - meta, fastq -> - single: fastq.size() == 1 - return [ meta, fastq.flatten() ] - multiple: fastq.size() > 1 - return [ meta, fastq.flatten() ] - } - .set { ch_fastq } - - // - // MODULE: Concatenate FastQ files from same sample if required - // - CAT_FASTQ ( - ch_fastq.multiple - ) - .reads - .mix(ch_fastq.single) - .set { ch_cat_fastq } - ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first()) - - // - // MODULE: Run FastQC - // - FASTQC ( - ch_cat_fastq - ) - ch_versions = ch_versions.mix(FASTQC.out.versions.first()) - - /* - * MODULE: Run TrimGalore! - */ - if (!params.skip_trimming) { - TRIMGALORE(ch_cat_fastq) - reads = TRIMGALORE.out.reads - ch_versions = ch_versions.mix(TRIMGALORE.out.versions.first()) - } else { - reads = ch_cat_fastq - } - - - - /* - * SUBWORKFLOW: Align reads, deduplicate and extract methylation with Bismark - */ - - // Aligner: bismark or bismark_hisat - if( params.aligner =~ /bismark/ ){ - - /* - * Run Bismark alignment + downstream processing - */ - BISMARK ( - reads, - PREPARE_GENOME.out.bismark_index, - params.skip_deduplication || params.rrbs, - params.cytosine_report || params.nomeseq - ) - ch_versions = ch_versions.mix(BISMARK.out.versions.unique{ it.baseName }) - ch_bam = BISMARK.out.bam - ch_dedup = BISMARK.out.dedup - ch_aligner_mqc = BISMARK.out.mqc - } - // Aligner: bwameth - else if ( params.aligner == 'bwameth' ){ - - BWAMETH ( - reads, - PREPARE_GENOME.out.bwameth_index, - PREPARE_GENOME.out.fasta, - PREPARE_GENOME.out.fasta_index, - params.skip_deduplication || params.rrbs, - ) - ch_versions = ch_versions.mix(BWAMETH.out.versions.unique{ it.baseName }) - ch_bam = BWAMETH.out.bam - ch_dedup = BWAMETH.out.dedup - ch_aligner_mqc = BWAMETH.out.mqc - } - - /* - * MODULE: Qualimap BamQC - */ - QUALIMAP_BAMQC ( - ch_dedup, - params.bamqc_regions_file ? Channel.fromPath( params.bamqc_regions_file, checkIfExists: true ).toList() : [] - ) - ch_versions = ch_versions.mix(QUALIMAP_BAMQC.out.versions.first()) - - /* - * MODULE: Run Preseq - */ - PRESEQ_LCEXTRAP ( - ch_bam - ) - ch_versions = ch_versions.mix(PRESEQ_LCEXTRAP.out.versions.first()) - - CUSTOM_DUMPSOFTWAREVERSIONS ( - ch_versions.unique().collectFile(name: 'collated_versions.yml') - ) - - // - // MODULE: MultiQC - // - if (!params.skip_multiqc) { - workflow_summary = WorkflowMethylseq.paramsSummaryMultiqc(workflow, summary_params) - ch_workflow_summary = Channel.value(workflow_summary) - - methods_description = WorkflowMethylseq.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params) - ch_methods_description = Channel.value(methods_description) - - ch_multiqc_files = Channel.empty() - ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) - ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) - ch_multiqc_files = ch_multiqc_files.mix(QUALIMAP_BAMQC.out.results.collect{ it[1] }.ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(PRESEQ_LCEXTRAP.out.log.collect{ it[1] }.ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(ch_aligner_mqc.ifEmpty([])) - if (!params.skip_trimming) { - ch_multiqc_files = ch_multiqc_files.mix(TRIMGALORE.out.log.collect{ it[1] }) - } - ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{ it[1] }.ifEmpty([])) - - MULTIQC ( - ch_multiqc_files.collect(), - ch_multiqc_config.toList(), - ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList() - ) - multiqc_report = MULTIQC.out.report.toList() - ch_versions = ch_versions.mix(MULTIQC.out.versions) - } -} - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - COMPLETION EMAIL AND SUMMARY -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -workflow.onComplete { - if (params.email || params.email_on_fail) { - NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report) - } - NfcoreTemplate.dump_parameters(workflow, params) - NfcoreTemplate.summary(workflow, params, log) - if (params.hook_url) { - NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log) - } -} - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - THE END -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ diff --git a/workflows/methylseq/main.nf b/workflows/methylseq/main.nf new file mode 100644 index 00000000..0cb93f59 --- /dev/null +++ b/workflows/methylseq/main.nf @@ -0,0 +1,198 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + + +include { FASTQC } from '../../modules/nf-core/fastqc/main' +include { TRIMGALORE } from '../../modules/nf-core/trimgalore/main' +include { QUALIMAP_BAMQC } from '../../modules/nf-core/qualimap/bamqc/main' +include { PRESEQ_LCEXTRAP } from '../../modules/nf-core/preseq/lcextrap/main' +include { MULTIQC } from '../../modules/nf-core/multiqc/main' +include { CAT_FASTQ } from '../../modules/nf-core/cat/fastq/main' +include { paramsSummaryMap } from 'plugin/nf-schema' +include { paramsSummaryMultiqc } from '../../subworkflows/nf-core/utils_nfcore_pipeline' +include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline' +include { methodsDescriptionText } from '../../subworkflows/local/utils_nfcore_methylseq_pipeline' +include { validateInputSamplesheet } from '../../subworkflows/local/utils_nfcore_methylseq_pipeline' +include { BISMARK } from '../../subworkflows/local/bismark/' +include { BWAMETH } from '../../subworkflows/local/bwameth' + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + RUN MAIN WORKFLOW +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +workflow METHYLSEQ { + + take: + samplesheet // channel: samplesheet read in from --input + ch_versions // channel: [ path(versions.yml) ] + ch_fasta // channel: path(genome.fasta) + ch_fasta_index // channel: path(star/index/) + ch_bismark_index // channel: path(star/index/) + ch_bwameth_index // channel: path(star/index/) + + main: + + ch_multiqc_files = Channel.empty() + + // + // Branch channels from input samplesheet channel + // + samplesheet + .branch { meta, fastqs -> + single : fastqs.size() == 1 + return [ meta, fastqs.flatten() ] + multiple: fastqs.size() > 1 + return [ meta, fastqs.flatten() ] + } + .set { ch_samplesheet } + + // + // MODULE: Concatenate FastQ files from same sample if required + // + CAT_FASTQ (ch_samplesheet.multiple) + .reads + .mix(ch_samplesheet.single) + .set {ch_fastq} + ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first()) + + // + // MODULE: Run FastQC + // + FASTQC (ch_fastq) + ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}) + ch_versions = ch_versions.mix(FASTQC.out.versions.first()) + + // + // MODULE: Run TrimGalore! + // + if (!params.skip_trimming) { + TRIMGALORE(ch_fastq) + reads = TRIMGALORE.out.reads + ch_versions = ch_versions.mix(TRIMGALORE.out.versions.first()) + } else { + reads = ch_fastq + } + + // + // SUBWORKFLOW: Align reads, deduplicate and extract methylation with Bismark + // + + // Aligner: bismark or bismark_hisat + if( params.aligner =~ /bismark/ ){ + // + // Run Bismark alignment + downstream processing + // + BISMARK ( + reads, + ch_fasta, + ch_bismark_index, + params.skip_deduplication || params.rrbs, + params.cytosine_report || params.nomeseq + ) + ch_versions = ch_versions.mix(BISMARK.out.versions.unique{ it.baseName }) + ch_bam = BISMARK.out.bam + ch_dedup = BISMARK.out.dedup + ch_aligner_mqc = BISMARK.out.mqc + } + // Aligner: bwameth + else if ( params.aligner == 'bwameth' ){ + + BWAMETH ( + reads, + ch_bwameth_index, + ch_fasta, + ch_fasta_index, + params.skip_deduplication || params.rrbs, + ) + ch_versions = ch_versions.mix(BWAMETH.out.versions.unique{ it.baseName }) + ch_bam = BWAMETH.out.bam + ch_dedup = BWAMETH.out.dedup + ch_aligner_mqc = BWAMETH.out.mqc + } + + // + // MODULE: Qualimap BamQC + // + QUALIMAP_BAMQC ( + ch_dedup, + params.bamqc_regions_file ? Channel.fromPath( params.bamqc_regions_file, checkIfExists: true ).toList() : [] + ) + ch_versions = ch_versions.mix(QUALIMAP_BAMQC.out.versions.first()) + + // + // MODULE: Run Preseq + // + PRESEQ_LCEXTRAP (ch_bam) + ch_versions = ch_versions.mix(PRESEQ_LCEXTRAP.out.versions.first()) + + // + // Collate and save software versions + // + softwareVersionsToYAML(ch_versions) + .collectFile( + storeDir: "${params.outdir}/pipeline_info", + name: 'nf_core_pipeline_software_mqc_versions.yml', + sort: true, + newLine: true + ).set { ch_collated_versions } + + // + // MODULE: MultiQC + // + ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) + ch_multiqc_custom_config = params.multiqc_config ? + Channel.fromPath(params.multiqc_config, checkIfExists: true) : + Channel.empty() + ch_multiqc_logo = params.multiqc_logo ? + Channel.fromPath(params.multiqc_logo, checkIfExists: true) : + Channel.empty() + + summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") + ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) + + ch_multiqc_custom_methods_description = params.multiqc_methods_description ? + file(params.multiqc_methods_description, checkIfExists: true) : + file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) + ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description)) + + ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) + ch_multiqc_files = ch_multiqc_files.mix( + ch_methods_description.collectFile( + name: 'methods_description_mqc.yaml', + sort: true + ) + ) + + ch_multiqc_files = ch_multiqc_files.mix(QUALIMAP_BAMQC.out.results.collect{ it[1] }.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(PRESEQ_LCEXTRAP.out.log.collect{ it[1] }.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(ch_aligner_mqc.ifEmpty([])) + if (!params.skip_trimming) { + ch_multiqc_files = ch_multiqc_files.mix(TRIMGALORE.out.log.collect{ it[1] }) + } + ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{ it[1] }.ifEmpty([])) + + MULTIQC ( + ch_multiqc_files.collect(), + ch_multiqc_config.toList(), + ch_multiqc_custom_config.toList(), + ch_multiqc_logo.toList(), + [], + [] + ) + + emit: + multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html + versions = ch_versions // channel: [ path(versions.yml) ] +} + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + THE END +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ diff --git a/workflows/methylseq/nextflow.config b/workflows/methylseq/nextflow.config new file mode 100644 index 00000000..e1ee85ad --- /dev/null +++ b/workflows/methylseq/nextflow.config @@ -0,0 +1,20 @@ + +includeConfig "../../subworkflows/local/bismark/nextflow.config" +includeConfig "../../subworkflows/local/bwameth/nextflow.config" +includeConfig "../../subworkflows/local/prepare_genome/nextflow.config" + +includeConfig "../../modules/nf-core/fastqc/nextflow.config" +includeConfig "../../modules/nf-core/trimgalore/nextflow.config" +includeConfig "../../modules/nf-core/multiqc/nextflow.config" +includeConfig "../../modules/nf-core/preseq/lcextrap/nextflow.config" +includeConfig "../../modules/nf-core/qualimap/bamqc/nextflow.config" + +process { + + publishDir = [ + path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + +}
    Process Name \\", - " \\ Software Version
    CUSTOM_DUMPSOFTWAREVERSIONSpython3.12.0
    yaml6.0.1
    TOOL1tool10.11.9
    TOOL2tool21.9
    WorkflowNextflow
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls