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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,18 +1,36 @@ | ||
| name: nf-core AWS full size tests | ||
| # This workflow is triggered on published releases. | ||
| # This workflow is triggered on PRs opened against the master branch. | ||
| # It can be additionally triggered manually with GitHub actions workflow dispatch button. | ||
| # It runs the -profile 'test_full' on AWS batch | ||
|
|
||
| on: | ||
| release: | ||
| types: [published] | ||
| pull_request: | ||
| branches: | ||
| - master | ||
| workflow_dispatch: | ||
| pull_request_review: | ||
| types: [submitted] | ||
|
|
||
| jobs: | ||
| run-platform: | ||
| name: Run AWS full tests | ||
| if: github.repository == 'nf-core/mag' | ||
| # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered | ||
| if: github.repository == 'nf-core/mag' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch' | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: octokit/[email protected] | ||
| if: github.event_name != 'workflow_dispatch' | ||
| id: check_approvals | ||
| with: | ||
| route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100 | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| - id: test_variables | ||
| if: github.event_name != 'workflow_dispatch' | ||
| run: | | ||
| JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}' | ||
| CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length') | ||
| test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required | ||
| - name: Launch workflow via Seqera Platform | ||
| uses: seqeralabs/action-tower-launch@v2 | ||
| with: | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| name: nf-core linting | ||
| # This workflow is triggered on pushes and PRs to the repository. | ||
| # It runs the `nf-core lint` and markdown lint tests to ensure | ||
| # It runs the `nf-core pipelines lint` and markdown lint tests to ensure | ||
| # that the code meets the nf-core guidelines. | ||
| on: | ||
| push: | ||
|
|
@@ -41,17 +41,32 @@ jobs: | |
| python-version: "3.12" | ||
| architecture: "x64" | ||
|
|
||
| - name: read .nf-core.yml | ||
| uses: pietrobolcato/[email protected] | ||
| id: read_yml | ||
| with: | ||
| config: ${{ github.workspace }}/.nf-core.yml | ||
|
|
||
| - name: Install dependencies | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install nf-core | ||
| pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} | ||
| - name: Run nf-core pipelines lint | ||
| if: ${{ github.base_ref != 'master' }} | ||
| env: | ||
| GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} | ||
| run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md | ||
|
|
||
| - name: Run nf-core lint | ||
| - name: Run nf-core pipelines lint --release | ||
| if: ${{ github.base_ref == 'master' }} | ||
| env: | ||
| GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} | ||
| run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md | ||
| run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md | ||
|
|
||
| - name: Save PR number | ||
| if: ${{ always() }} | ||
|
|
||
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