nextflow-stub-check.yaml

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@v3

      - name: Check Nextflow workflow
        uses: docker://nextflow/nextflow:21.10.6
        with:
          args: nextflow -log stub-run.log run main.nf -stub -profile stub -ansi-log false

      - name: Check Nextflow with checkpoints from previous run
        uses: docker://nextflow/nextflow:21.10.6
        with:
          args: nextflow -log checkpoint-run.log run main.nf -stub -profile stub -ansi-log false

      - name: Check Nextflow workflow for building cell type references
        uses: docker://nextflow/nextflow:21.10.6
        with:
          args: nextflow -log celltype-ref-run.log run build-celltype-ref.nf -stub -profile stub -ansi-log false

      - name: Join log files
        if: ${{ !cancelled() }}
        run: cat stub-run.log checkpoint-run.log celltype-ref-run.log > nextflow-runs.log

      - name: Upload nextflow log
        if: ${{ !cancelled() }}
        uses:  actions/upload-artifact@v3
        with:
          name: nextflow-log
          path: nextflow-runs.log