wip #5
Workflow file for this run
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| name: nf-core CI | |
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| on: | |
| pull_request: | |
| release: | |
| types: [published] | |
| merge_group: | |
| types: | |
| - checks_requested | |
| branches: | |
| - master | |
| - dev | |
| env: | |
| NFT_DIFF: "pdiff" | |
| NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2" | |
| NFT_VER: "0.9.0" | |
| NFT_WORKDIR: "~" | |
| NXF_ANSI_LOG: false | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }} | |
| TEST_DATA_BASE: "${{ github.workspace }}/test-datasets" | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| pytest-changes: | |
| name: Check for changes (pytest) | |
| runs-on: ubuntu-latest | |
| outputs: | |
| # Expose matched filters as job 'tags' output variable | |
| tags: ${{ steps.filter.outputs.changes }} | |
| steps: | |
| - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | |
| - uses: frouioui/paths-filter@main | |
| id: filter | |
| with: | |
| filters: "tests/config/pytesttags.yml" | |
| token: "" | |
| pytest: | |
| name: ${{ matrix.tags }} ${{ matrix.profile }} NF ${{ matrix.NXF_VER }} | |
| runs-on: ubuntu-latest | |
| needs: pytest-changes | |
| if: needs.pytest-changes.outputs.tags != '[]' | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tags: ["${{ fromJson(needs.pytest-changes.outputs.tags) }}"] | |
| profile: ["docker"] | |
| # profile: ["docker", "singularity", "conda"] | |
| TEST_DATA_BASE: | |
| - "test-datasets/data" | |
| NXF_VER: | |
| - "24.04.2" | |
| - "latest-everything" | |
| exclude: | |
| - tags: "sentieon/bwamem" | |
| - tags: "sentieon/dedup" | |
| - tags: "sentieon/dnascope" | |
| - tags: "sentieon/dnascope_joint_germline" | |
| - tags: "sentieon/dnascope_skip_filter" | |
| - tags: "sentieon/haplotyper" | |
| - tags: "sentieon/haplotyper_joint_germline" | |
| - tags: "sentieon/haplotyper_skip_filter" | |
| - NXF_VER: "latest-everything" | |
| tags: "joint_germline" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | |
| - name: Hash Github Workspace | |
| id: hash_workspace | |
| run: | | |
| echo "digest=$(echo sarek3_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT | |
| - name: Set up Python | |
| uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 | |
| with: | |
| python-version: "3.11" | |
| cache: "pip" | |
| cache-dependency-path: | | |
| **/requirements.txt | |
| - name: Install Python dependencies | |
| run: pip install --upgrade -r tests/requirements.txt | |
| - name: Install Nextflow ${{ matrix.NXF_VER }} | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Setup apptainer | |
| if: matrix.profile == 'singularity' | |
| uses: eWaterCycle/setup-apptainer@main | |
| - name: Set up Singularity | |
| if: matrix.profile == 'singularity' | |
| run: | | |
| mkdir -p $NXF_SINGULARITY_CACHEDIR | |
| mkdir -p $NXF_SINGULARITY_LIBRARYDIR | |
| - name: Set up miniconda | |
| if: matrix.profile == 'conda' | |
| uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| channels: conda-forge,bioconda | |
| - name: Conda setup | |
| if: matrix.profile == 'conda' | |
| run: | | |
| conda clean -a | |
| conda install -n base conda-libmamba-solver | |
| conda config --set solver libmamba | |
| echo $(realpath $CONDA)/condabin >> $GITHUB_PATH | |
| echo $(realpath python) >> $GITHUB_PATH | |
| - name: Cache test data | |
| id: cache-testdata | |
| uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 | |
| with: | |
| path: test-datasets/ | |
| key: ${{ steps.hash_workspace.outputs.digest }} | |
| - name: Check out test data | |
| if: steps.cache-testdata.outputs.cache-hit != 'true' | |
| uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | |
| with: | |
| repository: nf-core/test-datasets | |
| ref: sarek3 | |
| path: test-datasets/ | |
| - name: Replace remote paths in samplesheets | |
| run: | | |
| for f in tests/csv/3.0/*csv; do | |
| sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/modules/=${{ github.workspace }}/test-datasets/=g" $f | |
| echo "========== $f ============" | |
| cat $f | |
| echo "========================================" | |
| done; | |
| # Set up secrets | |
| - name: Set up nextflow secrets | |
| if: env.SENTIEON_LICENSE_BASE64 != null | |
| run: | | |
| nextflow secrets set SENTIEON_LICENSE_BASE64 ${{ secrets.SENTIEON_LICENSE_BASE64 }} | |
| nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }} | |
| SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d) | |
| SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d) | |
| SENTIEON_AUTH_DATA=$(python bin/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE") | |
| SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0) | |
| nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64 | |
| - name: Conda clean | |
| if: matrix.profile == 'conda' | |
| run: conda clean -a | |
| - name: Disk space cleanup | |
| uses: jlumbroso/[email protected] | |
| - name: Run pytest-workflow | |
| uses: Wandalen/wretry.action@v1 | |
| with: | |
| command: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes | |
| attempt_limit: 3 | |
| - name: Output log on failure | |
| if: failure() | |
| run: | | |
| sudo apt install bat > /dev/null | |
| batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err} | |
| - name: Upload logs on failure | |
| if: failure() | |
| uses: actions/upload-artifact@50769540e7f4bd5e21e526ee35c689e35e0d6874 # v4 | |
| with: | |
| name: logs-${{ matrix.profile }} | |
| path: | | |
| /home/ubuntu/pytest_workflow_*/*/.nextflow.log | |
| /home/ubuntu/pytest_workflow_*/*/log.out | |
| /home/ubuntu/pytest_workflow_*/*/log.err | |
| /home/ubuntu/pytest_workflow_*/*/work | |
| !/home/ubuntu/pytest_workflow_*/*/work/conda | |
| !/home/ubuntu/pytest_workflow_*/*/work/singularity | |
| !${{ github.workspace }}/.singularity | |
| nftest-changes: | |
| name: Check for changes (nf-test) | |
| runs-on: ubuntu-latest | |
| outputs: | |
| tags: ${{ steps.filter.outputs.changes }} | |
| steps: | |
| - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | |
| - name: Combine all tags.yml files | |
| id: get_tags | |
| run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml | |
| - uses: frouioui/paths-filter@main | |
| id: filter | |
| with: | |
| filters: ".github/tags.yml" | |
| token: "" | |
| nftest: | |
| name: ${{ matrix.tags }} ${{ matrix.profile }} NF ${{ matrix.NXF_VER }} | |
| runs-on: ubuntu-latest | |
| needs: nftest-changes | |
| if: needs.nftest-changes.outputs.tags != '[]' | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tags: ["${{ fromJson(needs.nftest-changes.outputs.tags) }}"] | |
| profile: ["docker"] | |
| # profile: ["docker", "singularity", "conda"] | |
| TEST_DATA_BASE: | |
| - "test-datasets/data" | |
| NXF_VER: | |
| - "24.04.2" | |
| - "latest-everything" | |
| exclude: | |
| - tags: "bcftools/annotate" | |
| - tags: "bcftools/concat" | |
| - tags: "bcftools/mpileup" | |
| - tags: "bcftools/sort" | |
| - tags: "bwa/index" | |
| - tags: "bwa/mem" | |
| - tags: "bwamem2/index" | |
| - tags: "bwamem2/mem" | |
| - tags: "cat/cat" | |
| - tags: "cat/fastq" | |
| - tags: "cnvkit/antitarget" | |
| - tags: "cnvkit/batch" | |
| - tags: "cnvkit/reference" | |
| - tags: "controlfreec/assesssignificance" | |
| - tags: "controlfreec/freec" | |
| - tags: "deepvariant/rundeepvariant" | |
| - tags: "dragmap/align" | |
| - tags: "dragmap/hashtable" | |
| - tags: "ensemblvep/download" | |
| - tags: "ensemblvep/vep" | |
| - tags: "fastp" | |
| - tags: "fastqc" | |
| - tags: "fgbio/callmolecularconsensusreads" | |
| - tags: "fgbio/fastqtobam" | |
| - tags: "freebayes" | |
| - tags: "gatk4/applybqsr" | |
| - tags: "gatk4/baserecalibrator" | |
| - tags: "gatk4/estimatelibrarycomplexity" | |
| - tags: "gatk4/genomicsdbimport" | |
| - tags: "gatk4/haplotypecaller" | |
| - tags: "gatk4/markduplicates" | |
| - tags: "gatk4/mergevcfs" | |
| - tags: "gatk4/mutect2" | |
| - tags: "gatk4spark/applybqsr" | |
| - tags: "gatk4spark/markduplicates" | |
| - tags: "gawk" | |
| - tags: "lofreq/callparallel" | |
| - tags: "mosdepth" | |
| - tags: "multiqc" | |
| - tags: "ngscheckmate/ncm" | |
| - tags: "samblaster" | |
| - tags: "samtools/convert" | |
| - tags: "samtools/mpileup" | |
| - tags: "samtools/stats" | |
| - tags: "sentieon/bwamem" | |
| - tags: "sentieon/haplotyper" | |
| - tags: "snpeff/snpeff" | |
| - tags: "spring/decompress" | |
| - tags: "strelka/germline" | |
| - tags: "strelka/somatic" | |
| - tags: "subworkflows/utils_nfvalidation_plugin" | |
| - tags: "svdb/merge" | |
| - tags: "tabix/bgziptabix" | |
| - tags: "tabix/tabix" | |
| - tags: "tiddit/sv" | |
| - tags: "untar" | |
| steps: | |
| - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | |
| - uses: actions/setup-java@2dfa2011c5b2a0f1489bf9e433881c92c1631f88 # v4 | |
| with: | |
| distribution: "temurin" | |
| java-version: "17" | |
| - name: Install Nextflow ${{ matrix.NXF_VER }} | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Install nf-test | |
| uses: nf-core/setup-nf-test@v1 | |
| with: | |
| version: ${{ env.NFT_VER }} | |
| - name: Setup apptainer | |
| if: matrix.profile == 'singularity' | |
| uses: eWaterCycle/setup-apptainer@main | |
| - name: Set up Singularity | |
| if: matrix.profile == 'singularity' | |
| run: | | |
| mkdir -p $NXF_SINGULARITY_CACHEDIR | |
| mkdir -p $NXF_SINGULARITY_LIBRARYDIR | |
| - name: Cache pdiff | |
| uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 | |
| id: cache-pip-pdiff | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-pdiff | |
| - name: Install pdiff | |
| run: python -m pip install --upgrade pip pdiff cryptography | |
| - name: Set up miniconda | |
| if: matrix.profile == 'conda' | |
| uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| channels: conda-forge,bioconda | |
| - name: Conda setup | |
| if: matrix.profile == 'conda' | |
| run: | | |
| conda clean -a | |
| conda install -n base conda-libmamba-solver | |
| conda config --set solver libmamba | |
| echo $(realpath $CONDA)/condabin >> $GITHUB_PATH | |
| echo $(realpath python) >> $GITHUB_PATH | |
| # Set up secrets | |
| - name: Set up nextflow secrets | |
| if: env.SENTIEON_LICENSE_BASE64 != null | |
| run: | | |
| nextflow secrets set SENTIEON_LICENSE_BASE64 ${{ secrets.SENTIEON_LICENSE_BASE64 }} | |
| nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }} | |
| SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d) | |
| SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d) | |
| SENTIEON_AUTH_DATA=$(python3 bin/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE") | |
| SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0) | |
| nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64 | |
| - name: Disk space cleanup | |
| uses: jlumbroso/[email protected] | |
| # Test the component | |
| - name: Run nf-test | |
| run: | | |
| nf-test test \ | |
| --profile="+${{ matrix.profile }}" \ | |
| --tag ${{ matrix.tags }} \ | |
| --tap=test.tap \ | |
| --junitxml=test.xml \ | |
| --debug \ | |
| --verbose | |
| confirm-pass: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - pytest | |
| - nftest | |
| if: always() | |
| steps: | |
| - name: All tests ok | |
| if: ${{ success() || !contains(needs.*.result, 'failure') }} | |
| run: exit 0 | |
| - name: One or more tests failed | |
| if: ${{ contains(needs.*.result, 'failure') }} | |
| run: exit 1 | |
| - name: debug-print | |
| if: always() | |
| run: | | |
| echo "toJSON(needs) = ${{ toJSON(needs) }}" | |
| echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" |