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nextflow-stub-check.yaml
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name: Check nextflow stub
on:
pull_request:
branches:
- main
- development
jobs:
nf-stub-check:
runs-on: ubuntu-22.04
steps:
- name: Checkout repo
uses: actions/checkout@v4
- name: Setup Nextflow
uses: nf-core/[email protected]
- name: Check Nextflow workflow
run: nextflow -log stub-run.log run main.nf -stub -profile stub -ansi-log false
- name: Check Nextflow with checkpoints from previous run
run: nextflow -log checkpoint-run.log run main.nf -stub -profile stub -ansi-log false
- name: Check Nextflow workflow for building cell type references
run: nextflow -log celltype-ref-run.log run build-celltype-ref.nf -stub -profile stub -ansi-log false
- name: Check Nextflow workflow for merging objects
run: nextflow -log merge-run.log run merge.nf -stub -profile stub -ansi-log false --project STUBP01
- name: Join log files
if: ${{ !cancelled() }}
run: cat stub-run.log checkpoint-run.log celltype-ref-run.log merge-run.log > nextflow-runs.log
- name: Upload nextflow log
if: ${{ !cancelled() }}
uses: actions/upload-artifact@v4
with:
name: nextflow-log
path: nextflow-runs.log