ci.yml

name: nf-core CI
# 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:
  release:
    types: [published]

jobs:
  test:
    name: Run workflow tests
    # Only run on push if this is the nf-core dev branch (merged PRs)
    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/sarek') }}
    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: ['20.07.1', '']
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v2
      - name: Check if Dockerfile or Conda environment changed
        uses: technote-space/get-diff-action@v1
        with:
          PREFIX_FILTER: |
            Dockerfile
            environment.yml
      - name: Build new docker image
        if: env.GIT_DIFF
        run: docker build --no-cache . -t nfcore/sarek:dev
      - name: Pull docker image
        if: ${{ !env.GIT_DIFF }}
        run: |
          docker pull nfcore/sarek:dev
          docker tag nfcore/sarek:dev nfcore/sarek:dev
      - name: Install Nextflow
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/
      - name: Run pipeline with test data
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile test,docker

  annotation:
    env:
      NXF_ANSI_LOG: false
    runs-on: ubuntu-latest
    strategy:
      matrix:
        tools: [snpeff, vep]
        species: [WBcel235]
    steps:
      - uses: actions/checkout@v2
      - name: Install Nextflow
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/
        env:
          # Only check Nextflow pipeline minimum version
          NXF_VER: '20.07.1'
      - name: Pull docker image
        run: |
          docker pull nfcore/sarek:dev
          docker pull nfcore/sarek${{ matrix.tools }}:dev.${{ matrix.species }}
      - name: Run annotation test
        run: nextflow run ${GITHUB_WORKSPACE} -profile test_annotation,docker --tools ${{ matrix.tools }}

  germline:
    env:
      NXF_ANSI_LOG: false
    runs-on: ubuntu-latest
    strategy:
      matrix:
        markduplicates: [--skip_markduplicates, '']
    steps:
      - uses: actions/checkout@v2
      - name: Install Nextflow
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/
        env:
          # Only check Nextflow pipeline minimum version
          NXF_VER: '20.07.1'
      - name: Pull docker image
        run: docker pull nfcore/sarek:dev
      - name: Get test data
        run: git clone --single-branch --branch sarek https://github.com/nf-core/test-datasets.git data
      - name: Run germline test
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.markduplicates }} --input data/testdata/tiny/normal --saved_bam_mapped
          nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.markduplicates }} --input=false --step prepare_recalibration -resume
          nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.markduplicates }} --input=false --step recalibrate -resume
          nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.markduplicates }} --input=false --step variantCalling

  minimal:
    env:
      NXF_ANSI_LOG: false
    runs-on: ubuntu-latest
    strategy:
      matrix:
        genome: [smallerGRCh37, minimalGRCh37]
        intervals: [--no_intervals, '']
    steps:
      - uses: actions/checkout@v2
      - name: Install Nextflow
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/
        env:
          # Only check Nextflow pipeline minimum version
          NXF_VER: '20.07.1'
      - name: Pull docker image
        run: docker pull nfcore/sarek:dev
      - name: Run test for minimal genomes
        run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --skipQC all --genome ${{ matrix.genome }} ${{ matrix.intervals }} --tools Manta,mpileup,Strelka,FreeBayes

  profile:
    env:
      NXF_ANSI_LOG: false
    runs-on: ubuntu-latest
    strategy:
      matrix:
        profile: [test_split_fastq, test_targeted, test_trimming, test_no_gatk_spark, test_umi_tso, test_umi_qiaseq]
    steps:
      - uses: actions/checkout@v2
      - name: Install Nextflow
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/
        env:
          # Only check Nextflow pipeline minimum version
          NXF_VER: '20.07.1'
      - name: Pull docker image
        run: docker pull nfcore/sarek:dev
      - name: Run ${{ matrix.profile }} test
        run: nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker

  aligner:
    env:
      NXF_ANSI_LOG: false
    runs-on: ubuntu-latest
    strategy:
      matrix:
        aligner: [bwa-mem, bwa-mem2]
    steps:
      - uses: actions/checkout@v2
      - name: Install Nextflow
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/
        env:
          # Only check Nextflow pipeline minimum version
          NXF_VER: '20.07.1'
      - name: Pull docker image
        run: docker pull nfcore/sarek:dev
      - name: Run ${{ matrix.profile }} test
        run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{ matrix.aligner }}

  tools:
    env:
      NXF_ANSI_LOG: false
    runs-on: ubuntu-latest
    strategy:
      matrix:
        tool: [Haplotypecaller, Freebayes, Manta, mpileup, MSIsensor, Strelka, TIDDIT]
        intervals: [--no_intervals, '']
        exclude:
          - tool: Manta
            intervals: --no_intervals
          - tool: MSIsensor
            intervals: --no_intervals
          - tool: Strelka
            intervals: --no_intervals
          - tool: TIDDIT
            intervals: --no_intervals
    steps:
      - uses: actions/checkout@v2
      - name: Install Nextflow
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/
        env:
          # Only check Nextflow pipeline minimum version
          NXF_VER: '20.07.1'
      - name: Pull docker image
        run: docker pull nfcore/sarek:dev
      - name: Run ${{ matrix.tool }} test
        run: nextflow run ${GITHUB_WORKSPACE} -profile test_tool,docker --tools ${{ matrix.tool }} ${{ matrix.intervals }}