ci_immcantation.yml

name: nf-core CI immcantation
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
on:
  push:
    branches:
      - dev
  pull_request:
    branches-ignore:
      - "master"

env:
  NXF_ANSI_LOG: false

concurrency:
  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
  cancel-in-progress: true

jobs:
  test_container:
    name: Run workflow with immcantation devel test_container
    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/airrflow') }}
    runs-on: ubuntu-latest
    strategy:
      matrix:
        NXF_VER:
          - "22.10.1"
          - "latest-everything"
        profile:
          [
            "test_assembled_immcantation_devel_hs",
            "test_assembled_immcantation_devel_mm",
            "test_raw_immcantation_devel",
          ]
      fail-fast: false
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v3

      - name: Install Nextflow
        uses: nf-core/setup-nextflow@v1
        with:
          version: "${{ matrix.NXF_VER }}"

      - name: Run pipeline with test data
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker --outdir ./results

      - name: Upload logs on failure
        if: failure()
        uses: actions/upload-artifact@v2
        with:
          name: logs-${{ matrix.profile }}
          path: |
            /home/runner/.nextflow.log
            /home/runner/work
            !/home/runner/work/conda
            !/home/runner/work/singularity