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Merge pull request #20 from nf-core/dev
First release PR
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,43 +1,124 @@ | ||
| name: nf-core CI | ||
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | ||
| name: nf-core CI | ||
| on: | ||
| push: | ||
| branches: | ||
| - dev | ||
| pull_request: | ||
| release: | ||
| types: [published] | ||
| merge_group: | ||
| types: | ||
| - checks_requested | ||
| branches: | ||
| - master | ||
| - dev | ||
|
|
||
| env: | ||
| NXF_ANSI_LOG: false | ||
| NFT_VER: "0.8.3" | ||
| NFT_WORKDIR: "~" | ||
| NFT_DIFF: "pdiff" | ||
| NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2" | ||
|
|
||
| concurrency: | ||
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | ||
| cancel-in-progress: true | ||
|
|
||
| jobs: | ||
| changes: | ||
| name: Check for changes | ||
| runs-on: ubuntu-latest | ||
| outputs: | ||
| # Expose matched filters as job 'tags' output variable | ||
| tags: ${{ steps.filter.outputs.changes }} | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - name: Combine all tags.yml files | ||
| id: get_username | ||
| run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml | ||
| - name: debug | ||
| run: cat .github/tags.yml | ||
| - uses: dorny/paths-filter@v2 | ||
| id: filter | ||
| with: | ||
| filters: ".github/tags.yml" | ||
|
|
||
| define_nxf_versions: | ||
| name: Choose nextflow versions to test against depending on target branch | ||
| runs-on: ubuntu-latest | ||
| outputs: | ||
| matrix: ${{ steps.nxf_versions.outputs.matrix }} | ||
| steps: | ||
| - id: nxf_versions | ||
| run: | | ||
| if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then | ||
| echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT | ||
| else | ||
| echo matrix='["latest-everything", "23.04.0"]' | tee -a $GITHUB_OUTPUT | ||
| fi | ||
| test: | ||
| name: Run pipeline with test data | ||
| # Only run on push if this is the nf-core dev branch (merged PRs) | ||
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/readsimulator') }}" | ||
| name: ${{ matrix.tags }} ${{ matrix.profile }} NF ${{ matrix.NXF_VER }} | ||
| needs: [changes, define_nxf_versions] | ||
| if: needs.changes.outputs.tags != '[]' | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| NXF_VER: | ||
| - "23.04.0" | ||
| - "latest-everything" | ||
| NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }} | ||
| tags: ["${{ fromJson(needs.changes.outputs.tags) }}"] | ||
| profile: | ||
| - "docker" | ||
|
|
||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v3 | ||
| uses: actions/checkout@v4 | ||
|
|
||
| - name: Install Nextflow | ||
| uses: nf-core/setup-nextflow@v1 | ||
| with: | ||
| version: "${{ matrix.NXF_VER }}" | ||
|
|
||
| - name: Run pipeline with test data | ||
| # 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 | ||
| - uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: "3.11" | ||
| architecture: "x64" | ||
|
|
||
| - name: Install pdiff to see diff between nf-test snapshots | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install pdiff | ||
| - name: Cache nf-test installation | ||
| id: cache-software | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: | | ||
| /usr/local/bin/nf-test | ||
| /home/runner/.nf-test/nf-test.jar | ||
| key: ${{ runner.os }}-${{ env.NFT_VER }}-nftest | ||
|
|
||
| - 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: Run nf-test | ||
| run: | | ||
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results | ||
| nf-test test --verbose --tag ${{ matrix.tags }} --profile test,"${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap | ||
| - uses: pcolby/tap-summary@v1 | ||
| with: | ||
| path: >- | ||
| test.tap | ||
| - name: Output log on failure | ||
| if: failure() | ||
| run: | | ||
| sudo apt install bat > /dev/null | ||
| batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log | ||
| - name: Publish Test Report | ||
| uses: mikepenz/action-junit-report@v3 | ||
| if: always() # always run even if the previous step fails | ||
| with: | ||
| report_paths: test.xml |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,67 @@ | ||
| name: Test successful pipeline download with 'nf-core download' | ||
|
|
||
| # Run the workflow when: | ||
| # - dispatched manually | ||
| # - when a PR is opened or reopened to master branch | ||
| # - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. | ||
| on: | ||
| workflow_dispatch: | ||
| pull_request: | ||
| types: | ||
| - opened | ||
| branches: | ||
| - master | ||
| pull_request_target: | ||
| branches: | ||
| - master | ||
|
|
||
| env: | ||
| NXF_ANSI_LOG: false | ||
|
|
||
| jobs: | ||
| download: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Install Nextflow | ||
| uses: nf-core/setup-nextflow@v1 | ||
|
|
||
| - uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: "3.11" | ||
| architecture: "x64" | ||
| - uses: eWaterCycle/setup-singularity@v7 | ||
| with: | ||
| singularity-version: 3.8.3 | ||
|
|
||
| - name: Install dependencies | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install git+https://github.com/nf-core/tools.git@dev | ||
| - name: Get the repository name and current branch set as environment variable | ||
| run: | | ||
| echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV} | ||
| echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} | ||
| echo "REPO_BRANCH=${GITHUB_REF#refs/heads/}" >> ${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 ./${{ env.REPOTITLE_LOWERCASE }} | ||
|
|
||
| - name: Run the downloaded pipeline | ||
| env: | ||
| NXF_SINGULARITY_CACHEDIR: ./ | ||
| NXF_SINGULARITY_HOME_MOUNT: true | ||
| run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -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/') && | ||
|
|
@@ -13,43 +13,77 @@ jobs: | |
| 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@b4ffde65f46336ab88eb53be808477a3936bae11 # 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 | ||
| run: gh pr checkout ${{ github.event.issue.number }} | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} | ||
|
|
||
| - uses: actions/setup-node@v3 | ||
| # Install and run pre-commit | ||
| - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 | ||
| with: | ||
| python-version: 3.11 | ||
|
|
||
| - 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 "[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 | ||
|
|
||
| - 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/readsimulator/actions/runs/${{ github.run_id }}) for more details. | ||
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