Add schema, validation, and better testing #2
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| name: Check Nextflow Workflow | |
| on: | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| nf-config-check: | |
| name: Check nextflow configuration | |
| runs-on: ubuntu-latest | |
| container: nfcore/tools:3.2.0 | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Check Nextflow params | |
| run: nextflow config | |
| - name: Check nextflow_schema.json file | |
| if: ${{ !cancelled() }} | |
| run: nf-core pipelines schema lint | |
| nf-stub-check: | |
| name: Check stub run | |
| runs-on: ubuntu-latest | |
| needs: nf-config-check | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Nextflow | |
| uses: nf-core/[email protected] | |
| - name: Check main workflow | |
| run: nextflow -log stub-run.log run main.nf -stub -profile stub -ansi-log false | |
| - name: Check simulate workflow | |
| run: nextflow -log simulate-run.log run main.nf -stub -profile stub -ansi-log false -entry simulate | |
| - name: Join log files | |
| if: ${{ !cancelled() }} | |
| run: cat stub-run.log simulate-run.log > nextflow-runs.log | |
| - name: Upload nextflow log | |
| if: ${{ !cancelled() }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: nextflow-log | |
| path: nextflow-runs.log |