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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| name: "Close user-tagged issues and PRs" | ||
| on: | ||
| schedule: | ||
| - cron: "0 0 * * 0" # Once a week | ||
|
|
||
| jobs: | ||
| clean-up: | ||
| runs-on: ubuntu-latest | ||
| permissions: | ||
| issues: write | ||
| pull-requests: write | ||
| steps: | ||
| - uses: actions/stale@v7 | ||
| 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." | ||
| close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity." | ||
| days-before-stale: 30 | ||
| days-before-close: 20 | ||
| days-before-pr-close: -1 | ||
| any-of-labels: "awaiting-changes,awaiting-feedback" | ||
| exempt-issue-labels: "WIP" | ||
| exempt-pr-labels: "WIP" | ||
| repo-token: ${{ secrets.GITHUB_TOKEN }} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,137 @@ | ||
| name: Create a pipeline from a template and test it | ||
| on: | ||
| push: | ||
| branches: | ||
| - dev | ||
| paths: | ||
| - nf_core/pipeline-template/** | ||
| pull_request: | ||
| release: | ||
| types: [published] | ||
|
|
||
| # Cancel if a newer run is started | ||
| concurrency: | ||
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | ||
| cancel-in-progress: true | ||
|
|
||
| env: | ||
| NXF_ANSI_LOG: false | ||
|
|
||
| jobs: | ||
| RunTestWorkflow: | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| NXF_ANSI_LOG: false | ||
| strategy: | ||
| matrix: | ||
| TEMPLATE: | ||
| - "template_skip_all.yml" | ||
| - "template_skip_github_badges.yml" | ||
| - "template_skip_igenomes.yml" | ||
| - "template_skip_ci.yml" | ||
| - "template_skip_nf_core_configs.yml" | ||
|
|
||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| name: Check out source-code repository | ||
|
|
||
| - name: Set up Python 3.11 | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: 3.11 | ||
|
|
||
| - name: Install python dependencies | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install . | ||
| - name: Install Nextflow | ||
| uses: nf-core/setup-nextflow@v1 | ||
| with: | ||
| version: latest-everything | ||
|
|
||
| # Install the Prettier linting tools | ||
| - uses: actions/setup-node@v3 | ||
|
|
||
| - name: Install Prettier | ||
| run: npm install -g prettier | ||
|
|
||
| # Install the editorconfig linting tools | ||
| - name: Install editorconfig-checker | ||
| run: npm install -g editorconfig-checker | ||
|
|
||
| # Create template files | ||
| - name: Create template skip all (except github) | ||
| run: | | ||
| printf "prefix: my-prefix\nskip: ['ci', 'github_badges', 'igenomes', 'nf_core_configs']" > template_skip_all.yml | ||
| - name: Create template skip github_badges | ||
| run: | | ||
| printf "prefix: my-prefix\nskip: github_badges" > template_skip_github_badges.yml | ||
| - name: Create template skip igenomes | ||
| run: | | ||
| printf "prefix: my-prefix\nskip: igenomes" > template_skip_igenomes.yml | ||
| - name: Create template skip ci | ||
| run: | | ||
| printf "prefix: my-prefix\nskip: ci" > template_skip_ci.yml | ||
| - name: Create template skip nf_core_configs | ||
| run: | | ||
| printf "prefix: my-prefix\nskip: nf_core_configs" > template_skip_nf_core_configs.yml | ||
| # Create a pipeline from the template | ||
| - name: create a pipeline from the template ${{ matrix.TEMPLATE }} | ||
| run: | | ||
| nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml ${{ matrix.TEMPLATE }} | ||
| - name: run the pipeline | ||
| run: | | ||
| nextflow run my-prefix-testpipeline -profile test,docker --outdir ./results | ||
| # Remove results folder before linting | ||
| - name: remove results folder | ||
| run: | | ||
| rm -rf ./results | ||
| # Try syncing it before we change anything | ||
| - name: nf-core sync | ||
| run: nf-core --log-file log.txt sync --dir my-prefix-testpipeline/ | ||
|
|
||
| # Run code style linting | ||
| - name: Run Prettier --check | ||
| run: prettier --check my-prefix-testpipeline | ||
|
|
||
| - name: Run ECLint check | ||
| run: editorconfig-checker -exclude README.md $(find my-prefix-testpipeline/.* -type f | grep -v '.git\|.py\|md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile') | ||
|
|
||
| # Remove TODO statements | ||
| - name: remove TODO | ||
| run: find my-prefix-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \; | ||
|
|
||
| # Replace zenodo.XXXXXX to pass readme linting | ||
| - name: replace zenodo.XXXXXX | ||
| run: find my-prefix-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \; | ||
|
|
||
| # Run nf-core linting | ||
| - name: nf-core lint | ||
| run: nf-core --log-file log.txt --hide-progress lint --dir my-prefix-testpipeline --fail-warned | ||
|
|
||
| # Run bump-version | ||
| - name: nf-core bump-version | ||
| run: nf-core --log-file log.txt bump-version --dir my-prefix-testpipeline/ 1.1 | ||
|
|
||
| # Run nf-core linting in release mode | ||
| - name: nf-core lint in release mode | ||
| run: nf-core --log-file log.txt --hide-progress lint --dir my-prefix-testpipeline --fail-warned --release | ||
|
|
||
| - name: Tar files | ||
| run: tar -cvf artifact_files.tar log.txt template_skip*.yml | ||
|
|
||
| - name: Upload log file artifact | ||
| if: ${{ always() }} | ||
| uses: actions/upload-artifact@v3 | ||
| with: | ||
| name: nf-core-log-file | ||
| path: artifact_files.tar |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -38,10 +38,10 @@ jobs: | |
| # Override to remove the default --check flag so that we make changes | ||
| options: "--color" | ||
|
|
||
| - name: Set up Python 3.8 | ||
| - name: Set up Python 3.11 | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: 3.8 | ||
| python-version: 3.11 | ||
| - name: python-isort | ||
| uses: isort/[email protected] | ||
| with: | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -76,12 +76,31 @@ jobs: | |
| - name: Check out source-code repository | ||
| uses: actions/checkout@v3 | ||
|
|
||
| - name: Set up Python 3.8 | ||
| - name: Set up Python 3.11 | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: 3.8 | ||
| python-version: 3.11 | ||
| - name: python-isort | ||
| uses: isort/[email protected] | ||
| with: | ||
| isortVersion: "latest" | ||
| requirementsFiles: "requirements.txt requirements-dev.txt" | ||
|
|
||
| static-type-check: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - uses: actions/setup-python@v3 | ||
| with: | ||
| python-version: "3.11" | ||
| - run: pip install mypy types-PyYAML | ||
| - name: Get Python changed files | ||
| id: changed-py-files | ||
| uses: tj-actions/changed-files@v23 | ||
| with: | ||
| files: | | ||
| *.py | ||
| **/*.py | ||
| - name: Run if any of the listed files above is changed | ||
| if: steps.changed-py-files.outputs.any_changed == 'true' | ||
| run: mypy ${{ steps.changed-py-files.outputs.all_changed_files }} --ignore-missing-imports | ||
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