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Merge pull request #34 from nf-core/nf-core-template-merge-3.0.2
Important! Template update for nf-core/tools v3.0.2
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,19 +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-tower: | ||
| run-platform: | ||
| name: Run AWS full tests | ||
| if: github.repository == 'nf-core/sammyseq' | ||
| # 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/sammyseq' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch' | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Launch workflow via tower | ||
| - uses: octokit/[email protected] | ||
| id: check_approvals | ||
| with: | ||
| route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews | ||
| 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 | ||
| # TODO nf-core: You can customise AWS full pipeline tests as required | ||
| # Add full size test data (but still relatively small datasets for few samples) | ||
|
|
@@ -31,9 +48,9 @@ jobs: | |
| } | ||
| profiles: test_full | ||
|
|
||
| - uses: actions/upload-artifact@v3 | ||
| - uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: Tower debug log file | ||
| name: Seqera Platform debug log file | ||
| path: | | ||
| tower_action_*.log | ||
| tower_action_*.json | ||
| seqera_platform_action_*.log | ||
| seqera_platform_action_*.json | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,119 @@ | ||
| name: Test successful pipeline download with 'nf-core pipelines 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: | ||
| inputs: | ||
| testbranch: | ||
| description: "The specific branch you wish to utilize for the test execution of nf-core pipelines download." | ||
| required: true | ||
| default: "dev" | ||
| pull_request: | ||
| types: | ||
| - opened | ||
| - edited | ||
| - synchronize | ||
| 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@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" | ||
|
|
||
| - name: Setup Apptainer | ||
| uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0 | ||
| with: | ||
| apptainer-version: 1.3.4 | ||
|
|
||
| - 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: Make a cache directory for the container images | ||
| run: | | ||
| mkdir -p ./singularity_container_images | ||
| - name: Download the pipeline | ||
| env: | ||
| NXF_SINGULARITY_CACHEDIR: ./singularity_container_images | ||
| run: | | ||
| nf-core pipelines 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 "community.wave.seqera.io" \ | ||
| --container-cache-utilisation 'amend' \ | ||
| --download-configuration 'yes' | ||
| - name: Inspect download | ||
| run: tree ./${{ env.REPOTITLE_LOWERCASE }} | ||
|
|
||
| - name: Count the downloaded number of container images | ||
| id: count_initial | ||
| run: | | ||
| image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) | ||
| echo "Initial container image count: $image_count" | ||
| echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV} | ||
| - name: Run the downloaded pipeline (stub) | ||
| id: stub_run_pipeline | ||
| continue-on-error: true | ||
| env: | ||
| NXF_SINGULARITY_CACHEDIR: ./singularity_container_images | ||
| NXF_SINGULARITY_HOME_MOUNT: true | ||
| run: nextflow run ./${{ 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: ${{ job.steps.stub_run_pipeline.status == failure() }} | ||
| env: | ||
| NXF_SINGULARITY_CACHEDIR: ./singularity_container_images | ||
| NXF_SINGULARITY_HOME_MOUNT: true | ||
| run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results | ||
|
|
||
| - name: Count the downloaded number of container images | ||
| id: count_afterwards | ||
| run: | | ||
| image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) | ||
| echo "Post-pipeline run container image count: $image_count" | ||
| echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV} | ||
| - name: Compare container image counts | ||
| run: | | ||
| if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then | ||
| initial_count=${{ env.IMAGE_COUNT_INITIAL }} | ||
| final_count=${{ env.IMAGE_COUNT_AFTER }} | ||
| difference=$((final_count - initial_count)) | ||
| echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!" | ||
| tree ./singularity_container_images | ||
| exit 1 | ||
| else | ||
| echo "The pipeline can be downloaded successfully!" | ||
| fi |
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