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Merge pull request #233 from qbic-pipelines/dev
Release 2.3
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,4 @@ | ||
| contact_links: | ||
| - name: Join nf-core | ||
| url: https://nf-co.re/join | ||
| about: Please join the nf-core community here |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,86 @@ | ||
| name: Test successful pipeline download with 'nf-core download' | ||
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| # 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 download." | ||
| required: true | ||
| default: "dev" | ||
| pull_request: | ||
| types: | ||
| - opened | ||
| - edited | ||
| - synchronize | ||
| branches: | ||
| - master | ||
| pull_request_target: | ||
| branches: | ||
| - master | ||
|
|
||
| env: | ||
| NXF_ANSI_LOG: false | ||
|
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||
| 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" | ||
| - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 | ||
| with: | ||
| singularity-version: 3.8.3 | ||
|
|
||
| - 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: Download the pipeline | ||
| env: | ||
| NXF_SINGULARITY_CACHEDIR: ./ | ||
| run: | | ||
| nf-core 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 "ghcr.io" \ | ||
| --container-cache-utilisation 'amend' \ | ||
| --download-configuration | ||
| - name: Inspect download | ||
| run: tree ./${{ env.REPOTITLE_LOWERCASE }} | ||
|
|
||
| - name: Run the downloaded pipeline (stub) | ||
| id: stub_run_pipeline | ||
| continue-on-error: true | ||
| env: | ||
| NXF_SINGULARITY_CACHEDIR: ./ | ||
| NXF_SINGULARITY_HOME_MOUNT: true | ||
| run: nextflow run ./${{ 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: ${{ job.steps.stub_run_pipeline.status == failure() }} | ||
| env: | ||
| NXF_SINGULARITY_CACHEDIR: ./ | ||
| NXF_SINGULARITY_HOME_MOUNT: true | ||
| run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results |
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| Original file line number | Diff line number | Diff line change |
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@@ -4,52 +4,86 @@ on: | |
| types: [created] | ||
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| 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/') && | ||
| contains(github.event.comment.body, '@nf-core-bot fix linting') && | ||
| github.repository == 'nf-core/rnadeseq' | ||
| github.repository == 'qbic-pipelines/rnadeseq' | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| # Use the @nf-core-bot token to check out so we can push later | ||
| - uses: actions/checkout@v3 | ||
| - 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 | ||
|
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| # 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 | ||
| run: gh pr checkout ${{ github.event.issue.number }} | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} | ||
|
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||
| - uses: actions/setup-node@v3 | ||
| # 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" | ||
|
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| - 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 "[email protected]" | ||
| 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 | ||
|
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||
| - 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 | ||
|
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||
| - 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/qbic-pipelines/rnadeseq/actions/runs/${{ github.run_id }}) for more details. | ||
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