Fix duplicate -b short flag in pipelines sync
#808
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| name: Update Template snapshots from a comment | |
| on: | |
| issue_comment: | |
| types: [created] # Add "@nf-core-bot update template snapshots" as a PR comment to trigger this workflow. | |
| jobs: | |
| prepare-matrix: | |
| name: Retrieve all template features | |
| runs-on: ubuntu-latest | |
| permissions: | |
| pull-requests: write | |
| outputs: | |
| all_features: ${{ steps.create_matrix.outputs.matrix }} | |
| steps: | |
| - name: branch-deploy | |
| id: branch-deploy | |
| uses: github/branch-deploy@fded0351b6b79f854b335c11b3d93063461dd288 # v11.1.2 | |
| with: | |
| trigger: "@nf-core-bot update template snapshots" | |
| reaction: "eyes" | |
| stable_branch: "dev" | |
| - name: checkout | |
| uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 | |
| - name: Create Matrix | |
| id: create_matrix | |
| run: | | |
| echo "matrix=$(yq '.[].features | keys | filter(. != "github") | filter(. != "is_nfcore") | filter(. != "test_config")' nf_core/pipelines/create/template_features.yml | \ | |
| yq 'flatten | tojson(0)' -)" >> $GITHUB_OUTPUT | |
| update-snapshots: | |
| needs: [prepare-matrix] | |
| runs-on: ubuntu-latest | |
| permissions: | |
| pull-requests: write | |
| strategy: | |
| matrix: | |
| TEMPLATE: ${{ fromJson(needs.prepare-matrix.outputs.all_features) }} | |
| include: | |
| - TEMPLATE: all | |
| fail-fast: false | |
| steps: | |
| # Use the @nf-core-bot token to check out so we can push later | |
| - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 | |
| with: | |
| token: ${{ secrets.nf_core_bot_auth_token }} | |
| # 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 }} | |
| # Install dependencies and run pytest | |
| - name: Set up Python | |
| uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6 | |
| with: | |
| python-version: "3.14" | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0 | |
| with: | |
| enable-cache: true | |
| - name: Install dependencies | |
| run: uv sync --all-extras | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3 | |
| with: | |
| version: latest-everything | |
| - name: Install nf-test | |
| uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2 | |
| with: | |
| version: "0.9.4" | |
| install-pdiff: true | |
| # Create template files | |
| - name: Create template skip ${{ matrix.TEMPLATE }} | |
| run: | | |
| mkdir -p create-test-lint-wf | |
| export NXF_WORK=$(pwd) | |
| if [ ${{ matrix.TEMPLATE }} == "all" ] | |
| then | |
| printf "org: my-prefix\nskip_features: ${{ needs.prepare-matrix.outputs.all_features }}" > create-test-lint-wf/template_skip_all.yml | |
| else | |
| printf "org: my-prefix\nskip_features: [${{ matrix.TEMPLATE }}]" > create-test-lint-wf/template_skip_${{ matrix.TEMPLATE }}.yml | |
| fi | |
| # Create a pipeline from the template | |
| - name: create a pipeline from the template ${{ matrix.TEMPLATE }} | |
| run: | | |
| cd create-test-lint-wf | |
| uv run nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --template-yaml template_skip_${{ matrix.TEMPLATE }}.yml | |
| # Copy snapshot file | |
| - name: copy snapshot file | |
| if: ${{ matrix.TEMPLATE != 'all' && matrix.TEMPLATE != 'nf-test' }} | |
| run: | | |
| if [ ! -f ${{ github.workspace }}/.github/snapshots/${{ matrix.TEMPLATE }}.nf.test.snap ]; then | |
| echo "Generate a snapshot when creating a pipeline and skipping the feature ${{ matrix.TEMPLATE }}." | |
| echo "Then, copy it to the directory .github/snapshots" | |
| else | |
| cp ${{ github.workspace }}/.github/snapshots/${{ matrix.TEMPLATE }}.nf.test.snap create-test-lint-wf/my-prefix-testpipeline/tests/default.nf.test.snap | |
| fi | |
| # Run pipeline with nf-test | |
| - name: run pipeline nf-test | |
| if: ${{ matrix.TEMPLATE != 'all' && matrix.TEMPLATE != 'nf-test' }} | |
| id: nf-test | |
| shell: bash | |
| run: | | |
| cd create-test-lint-wf/my-prefix-testpipeline | |
| nf-test test \ | |
| --profile=+docker \ | |
| --verbose \ | |
| --update-snapshot | |
| - name: Copy snapshot to .github/snapshots | |
| if: steps.nf-test.outcome == 'success' | |
| run: | | |
| cp create-test-lint-wf/my-prefix-testpipeline/tests/default.nf.test.snap .github/snapshots/${{ matrix.TEMPLATE }}.nf.test.snap | |
| - name: Upload snapshot artifact | |
| if: steps.nf-test.outcome == 'success' | |
| uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 | |
| with: | |
| name: snapshot-${{ matrix.TEMPLATE }} | |
| path: .github/snapshots/${{ matrix.TEMPLATE }}.nf.test.snap | |
| # indication that the run has finished | |
| - name: react if finished succesfully | |
| if: steps.nf-test.outcome == 'success' | |
| uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 | |
| with: | |
| comment-id: ${{ github.event.comment.id }} | |
| reactions: "+1" | |
| commit-snapshots: | |
| needs: [prepare-matrix, update-snapshots] | |
| runs-on: ubuntu-latest | |
| if: always() && needs.update-snapshots.result != 'skipped' | |
| steps: | |
| - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6 | |
| with: | |
| token: ${{ secrets.nf_core_bot_auth_token }} | |
| - name: Checkout Pull Request | |
| run: gh pr checkout ${{ github.event.issue.number }} | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} | |
| - name: Download all snapshot artifacts | |
| uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8 | |
| with: | |
| pattern: snapshot-* | |
| path: .github/snapshots/ | |
| merge-multiple: true | |
| - name: Commit & push changes | |
| id: commit-and-push | |
| run: | | |
| git config user.email "core@nf-co.re" | |
| git config user.name "nf-core-bot" | |
| git add .github/snapshots/ | |
| git diff --staged --quiet && echo "No snapshot changes to commit" && exit 0 | |
| git commit -m "[automated] Update Template snapshots" | |
| git push | |
| - name: react if snapshots were updated | |
| id: react-if-updated | |
| if: steps.commit-and-push.outcome == 'success' | |
| uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 | |
| with: | |
| comment-id: ${{ github.event.comment.id }} | |
| reactions: hooray | |
| - name: react if snapshots were not updated | |
| if: steps.commit-and-push.outcome == 'failure' | |
| uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 | |
| with: | |
| comment-id: ${{ github.event.comment.id }} | |
| reactions: confused | |
| - name: react if snapshots were not updated | |
| if: steps.commit-and-push.outcome == 'failure' | |
| uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5 | |
| with: | |
| issue-number: ${{ github.event.issue.number }} | |
| body: | | |
| @${{ github.actor }} I tried to update the snapshots, but it didn't work. Please update them manually. |