PR for release 1.0.0

.github/.dockstore.yml

@@ -0,0 +1,5 @@
+# Dockstore config version, not pipeline version
+version: 1.2
+workflows:
+  - subclass: nfl
+    primaryDescriptorPath: /nextflow.config

.github/CONTRIBUTING.md

@@ -1,22 +1,23 @@
-# steffenlem/sradownloader: Contributing Guidelines
+# qbic-pipelines/sradownloader: Contributing Guidelines
 
 Hi there!
-Many thanks for taking an interest in improving steffenlem/sradownloader.
+Many thanks for taking an interest in improving nf-core/sradownloader.
 
-We try to manage the required tasks for steffenlem/sradownloader using GitHub issues, you probably came to this page when creating one.
+We try to manage the required tasks for nf-core/sradownloader using GitHub issues, you probably came to this page when creating one.
 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 ;)
 
+> If you need help using or modifying nf-core/sradownloader then the best place to ask is on the nf-core Slack [#sradownloader](https://nfcore.slack.com/channels/sradownloader) channel ([join our Slack here](https://nf-co.re/join/slack)).
 
 ## Contribution workflow
 
-If you'd like to write some code for steffenlem/sradownloader, the standard workflow is as follows:
+If you'd like to write some code for nf-core/sradownloader, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [steffenlem/sradownloader issues](https://github.com/steffenlem/sradownloader/issues) to avoid duplicating work
+1. Check that there isn't already an issue about your idea in the [nf-core/sradownloader issues](https://github.com/nf-core/sradownloader/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 [steffenlem/sradownloader repository](https://github.com/steffenlem/sradownloader) to your GitHub account
+2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/sradownloader repository](https://github.com/nf-core/sradownloader) to your GitHub account
 3. Make the necessary changes / additions within your forked repository
 4. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
 
@@ -45,9 +46,12 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Patch
 
-: warning: Only in the unlikely and regretful event of a release happening with a bug.
+:warning: Only in the unlikely and regretful event of a release happening with a bug.
 
 * On your own fork, make a new branch `patch` based on `upstream/master`.
 * Fix the bug, and bump version (X.Y.Z+1).
 * A PR should be made on `master` from patch to directly this particular bug.
 
+## Getting help
+
+For further information/help, please consult the [nf-core/sradownloader documentation](https://nf-co.re/sradownloader/usage) and don't hesitate to get in touch on the nf-core Slack [#sradownloader](https://nfcore.slack.com/channels/sradownloader) channel ([join our Slack here](https://nf-co.re/join/slack)).

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,24 +1,32 @@
-# steffenlem/sradownloader bug report
+---
+name: Bug report
+about: Report something that is broken or incorrect
+labels: bug
+---
+
+<!--
+# qbic-pipelines/sradownloader bug report
 
 Hi there!
 
 Thanks for telling us about a problem with the pipeline.
 Please delete this text and anything that's not relevant from the template below:
+-->
 
-## Describe the bug
+## Description of the bug
 
-A clear and concise description of what the bug is.
+<!-- A clear and concise description of what the bug is. -->
 
 ## Steps to reproduce
 
 Steps to reproduce the behaviour:
 
-1. Command line: `nextflow run ...`
-2. See error: _Please provide your error message_
+1. Command line: <!-- [e.g. `nextflow run ...`] -->
+2. See error: <!-- [Please provide your error message] -->
 
 ## Expected behaviour
 
-A clear and concise description of what you expected to happen.
+<!-- A clear and concise description of what you expected to happen. -->
 
 ## System
 
@@ -33,10 +41,10 @@ A clear and concise description of what you expected to happen.
 
 ## Container engine
 
-- Engine: <!-- [e.g. Conda, Docker or Singularity] -->
+- Engine: <!-- [e.g. Conda, Docker, Singularity or Podman] -->
 - version: <!-- [e.g. 1.0.0] -->
 - Image tag: <!-- [e.g. nfcore/sradownloader:1.0.0] -->
 
 ## Additional context
 
-Add any other context about the problem here.
+<!-- Add any other context about the problem here. -->

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,8 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Join nf-core
+    url: https://nf-co.re/join
+    about: Please join the nf-core community here
+  - name: "Slack #sradownloader channel"
+    url: https://nfcore.slack.com/channels/sradownloader
+    about: Discussion about the nf-core/sradownloader pipeline

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,24 +1,32 @@
-# steffenlem/sradownloader feature request
+---
+name: Feature request
+about: Suggest an idea for the qbic-pipelines website
+labels: enhancement
+---
+
+<!--
+# qbic-pipelines/sradownloader feature request
 
 Hi there!
 
 Thanks for suggesting a new feature for the pipeline!
 Please delete this text and anything that's not relevant from the template below:
+-->
 
 ## Is your feature request related to a problem? Please describe
 
-A clear and concise description of what the problem is.
+<!-- A clear and concise description of what the problem is. -->
 
-Ex. I'm always frustrated when [...]
+<!-- e.g. [I'm always frustrated when ...] -->
 
 ## Describe the solution you'd like
 
-A clear and concise description of what you want to happen.
+<!-- A clear and concise description of what you want to happen. -->
 
 ## Describe alternatives you've considered
 
-A clear and concise description of any alternative solutions or features you've considered.
+<!-- A clear and concise description of any alternative solutions or features you've considered. -->
 
 ## Additional context
 
-Add any other context about the feature request here.
+<!-- Add any other context about the feature request here. -->

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,19 +1,19 @@
-# steffenlem/sradownloader pull request
+<!--
+# qbic-pipelines/sradownloader pull request
 
-Many thanks for contributing to steffenlem/sradownloader!
+Many thanks for contributing to qbic-pipelines/sradownloader!
 
 Please fill in the appropriate checklist below (delete whatever is not relevant).
 These are the most common things requested on pull requests (PRs).
 
-## PR checklist
+Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
+
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/qbic-pipelines/sradownloader/tree/master/.github/CONTRIBUTING.md)
+-->
+
+# PR checklist
 
 - [ ] This comment contains a description of changes (with reason)
+- [ ] `CHANGELOG.md` is updated
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If necessary, also make a PR on the [steffenlem/sradownloader branch on the nf-core/test-datasets repo](https://github.com/nf-core/test-datasets/pull/new/steffenlem/sradownloader)
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
-- [ ] Make sure your code lints (`nf-core lint .`).
 - [ ] Documentation in `docs` is updated
-- [ ] `CHANGELOG.md` is updated
-- [ ] `README.md` is updated
-
-**Learn more about contributing:** [CONTRIBUTING.md](https://github.com/steffenlem/sradownloader/tree/master/.github/CONTRIBUTING.md)

.github/workflows/awsfulltest.yml

@@ -0,0 +1,43 @@
+name: nf-core AWS full size tests
+# This workflow is triggered on published releases.
+# It can be additionally triggered manually with GitHub actions workflow dispatch.
+# It runs the -profile 'test_full' on AWS batch
+
+on:
+  workflow_run:
+    workflows: ["nf-core Docker push (release)"]
+    types: [completed]
+  workflow_dispatch:
+
+jobs:
+  run-awstest:
+    name: Run AWS full tests
+    if: github.repository == 'nf-core/sradownloader'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Setup Miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: 3.7
+      - name: Install awscli
+        run: conda install -c conda-forge awscli
+      - name: Start AWS batch job
+        # TODO nf-core: You can customise AWS full pipeline tests as required
+        # Add full size test data (but still relatively small datasets for few samples)
+        # on the `test_full.config` test runs with only one set of parameters
+        # Then specify `-profile test_full` instead of `-profile test` on the AWS batch command
+        env:
+          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
+          AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
+          AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
+          AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
+        run: |
+          aws batch submit-job \
+            --region eu-west-1 \
+            --job-name nf-core-sradownloader \
+            --job-queue $AWS_JOB_QUEUE \
+            --job-definition $AWS_JOB_DEFINITION \
+            --container-overrides '{"command": ["nf-core/sradownloader", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/sradownloader/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/sradownloader/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'

.github/workflows/awstest.yml

@@ -0,0 +1,39 @@
+name: nf-core AWS test
+# This workflow is triggered on push to the master branch.
+# It can be additionally triggered manually with GitHub actions workflow dispatch.
+# It runs the -profile 'test' on AWS batch.
+
+on:
+  workflow_dispatch:
+
+jobs:
+  run-awstest:
+    name: Run AWS tests
+    if: github.repository == 'nf-core/sradownloader'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Setup Miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: 3.7
+      - name: Install awscli
+        run: conda install -c conda-forge awscli
+      - name: Start AWS batch job
+        # TODO nf-core: You can customise CI pipeline run tests as required
+        # For example: adding multiple test runs with different parameters
+        # Remember that you can parallelise this by using strategy.matrix
+        env:
+          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }}
+          AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }}
+          AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }}
+          AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }}
+        run: |
+          aws batch submit-job \
+          --region eu-west-1 \
+          --job-name nf-core-sradownloader \
+          --job-queue $AWS_JOB_QUEUE \
+          --job-definition $AWS_JOB_DEFINITION \
+          --container-overrides '{"command": ["nf-core/sradownloader", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/sradownloader/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/sradownloader/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'

.github/workflows/branch.yml

@@ -2,15 +2,36 @@ name: nf-core branch protection
 # This workflow is triggered on PRs to master branch on the repository
 # It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
 on:
-  pull_request:
-    branches:
-    - master
+  pull_request_target:
+    branches: [master]
 
 jobs:
   test:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     steps:
-      # PRs are only ok if coming from an nf-core `dev` branch or a fork `patch` branch
+      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
+        if: github.repository == 'qbic-pipelines/sradownloader'
         run: |
-          { [[ $(git remote get-url origin) == *steffenlem/sradownloader ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]]; } || [[ ${GITHUB_HEAD_REF} == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name}} == qbic-pipelines/sradownloader ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+
+
+      # If the above check failed, post a comment on the PR explaining the failure
+      # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
+      - name: Post PR comment
+        if: failure()
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            Hi @${{ github.event.pull_request.user.login }},
+
+            It looks like this pull-request is has been made against the ${{github.event.pull_request.head.repo.full_name}} `master` branch.
+            The `master` branch on qbic-pipelines repositories should always contain code from the latest release.
+            Because of this, PRs to `master` are only allowed if they come from the ${{github.event.pull_request.head.repo.full_name}} `dev` branch.
+
+            You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
+
+            Thanks again for your contribution!
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          allow-repeats: false
+

.github/workflows/ci.yml

@@ -1,30 +1,56 @@
 name: nf-core CI
-# This workflow is triggered on pushes and PRs to the repository.
-# It runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
-on: [push, pull_request]
+# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+on:
+  push:
+    branches:
+      - dev
+  pull_request:
+  release:
+    types: [published]
 
 jobs:
   test:
+    name: Run workflow tests
+    # Only run on push if this is the qbic-pipelines dev branch (merged PRs)
+    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'qbic-pipelines/sradownloader') }}
+    runs-on: ubuntu-latest
     env:
       NXF_VER: ${{ matrix.nxf_ver }}
       NXF_ANSI_LOG: false
-    runs-on: ubuntu-latest
     strategy:
       matrix:
         # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ['19.10.0', '']
+        nxf_ver: ['20.04.0', '']
     steps:
-      - uses: actions/checkout@v2
+      - name: Check out pipeline code
+        uses: actions/checkout@v2
+
+      - name: Check if Dockerfile or Conda environment changed
+        uses: technote-space/get-diff-action@v4
+        with:
+          FILES: |
+            Dockerfile
+            environment.yml
+
+      - name: Build new docker image
+        if: env.MATCHED_FILES
+        run: docker build --no-cache . -t qbicpipelines/sradownloader:1.0.0
+
+      - name: Pull docker image
+        if: ${{ !env.MATCHED_FILES }}
+        run: |
+          docker pull qbicpipelines/sradownloader:dev
+          docker tag qbicpipelines/sradownloader:dev qbicpipelines/sradownloader:1.0.0
+
       - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
-      - name: Pull docker image
-        run: |
-          docker pull steffenlem/sradownloader:latest
-          docker tag steffenlem/sradownloader:latest steffenlem/sradownloader:latest
+
       - name: Run pipeline with test data
+        # For example: adding multiple test runs with different parameters
+        # Remember that you can parallelise this by using strategy.matrix
         run: |
-          # TODO nf-core: You can customise CI pipeline run tests as required
-          # (eg. adding multiple test runs with different parameters)
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker