ci.yml

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

env:
  NXF_ANSI_LOG: false
  NFTEST_VER: "0.7.3"

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

jobs:
  test:
    name: Run pipeline with test data
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        NXF_VER:
          - "23.04.0"
          - "latest-everything"
        aligner:
          - "bismark"
          - "bismark_hisat"
          - "bwameth"
        profile:
          - "docker"
    steps:
      # Skip if it's a pull_request to dev and NXF_VER is '22.10.1'
      - name: Skip condition
        id: condition
        run: |
          if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
            echo "skip=true" >> $GITHUB_OUTPUT
          fi

      - name: Check out pipeline code
        if: steps.condition.outputs.skip != 'true'
        uses: actions/checkout@v3

      - name: Hash Github Workspace
        if: steps.condition.outputs.skip != 'true'
        id: hash_workspace
        run: |
          echo "digest=$(echo methylseq2_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT

      - name: Cache test data
        if: steps.condition.outputs.skip != 'true'
        id: cache-testdata
        uses: actions/cache@v3
        with:
          path: test-datasets/
          key: ${{ steps.hash_workspace.outputs.digest }}

      - name: Check out test data
        if: steps.cache-testdata.outputs.cache-hit != 'true' && steps.condition.outputs.skip != 'true'
        uses: actions/checkout@v3
        with:
          repository: nf-core/test-datasets
          ref: methylseq
          path: test-datasets/

      - name: Replace remote paths in samplesheets
        if: steps.condition.outputs.skip != 'true'
        run: |
          for f in ./test-datasets/samplesheet/*csv; do
            sed -i 's=https://github.com/nf-core/test-datasets/raw/methylseq/=./test-datasets/=g' $f
            sed -i 's=https://raw.githubusercontent.com/nf-core/test-datasets/methylseq/=./test-datasets/=g' $f
            echo "========== $f ============"
            cat $f
            echo "========================================"
          done;

      - name: Install Nextflow
        if: steps.condition.outputs.skip != 'true'
        uses: nf-core/setup-nextflow@v1
        with:
          version: "${{ matrix.NXF_VER }}"

      - name: Install nf-test
        if: steps.condition.outputs.skip != 'true'
        run: |
          wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
          sudo mv nf-test /usr/local/bin/

      - name: Run nf-test
        if: steps.condition.outputs.skip != 'true'
        run: |
          nf-test test tests/pipeline/${{ matrix.aligner }}/ --profile "test,${{ matrix.profile }}" --tap=test.tap

      # If the test fails, output the software_versions.yml using the 'batcat' utility
      - name: Output log on failure
        if: failure()
        run: |
          sudo apt install bat > /dev/null
          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml