main.yml

name: Main
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
on:
  push:
    branches:
      - dev
      - 15-cicd-tests
  pull_request:
  release:
    types: [published]

# Uncomment if we need an edge release of Nextflow again
# env: NXF_EDGE: 1

jobs:
  test:
    name: Run workflow tests
    runs-on: ubuntu-latest
    env:
      NXF_VER: ${{ matrix.nxf_ver }}
      NXF_ANSI_LOG: false
    strategy:
      matrix:
        # Nextflow versions: check pipeline minimum and current latest
        nxf_ver: ["22.10.6"]
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v3

      - name: Install Nextflow
        env:
          CAPSULE_LOG: none
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/
      - name: HELPTEXT Run with the help flag
        run: |
          nextflow run ${GITHUB_WORKSPACE} --help
      - name: DELAY to try address some odd behaviour with what appears to be a conflict between parallel htslib jobs leading to CI hangs
        run: |
          if [[ $NXF_VER = '' ]]; then sleep 1200; fi
      - name: BASIC Run the basic pipeline only for ACE calling with docker
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
      - name: BASIC Run the basic pipeline only for ACE calling with singularity
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile test,singularity