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]
  workflow_dispatch:

env:
  NXF_ANSI_LOG: false
  NFT_VER: "0.9.2"
  NFT_WORKDIR: "~"
  NFT_DIFF: "pdiff"
  NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity

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

jobs:
  nf-test-changes:
    name: nf-test-changes
    runs-on: ubuntu-latest
    outputs:
      paths: ${{ steps.list.outputs.paths }}
    steps:
      - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
        run: |
          ls -la ./
          rm -rf ./* || true
          rm -rf ./.??* || true
          ls -la ./

      - uses: actions/checkout@v4
        with:
          fetch-depth: 0

      - name: Install pdiff to see diff between nf-test snapshots
        run: |
          python -m pip install --upgrade pip
          pip install pdiff

      - uses: nf-core/setup-nf-test@v1
        with:
          version: ${{ env.NFT_VER }}

      - name: List nf-test files
        id: list
        run: |
          COMPONENTS=$(nf-test list --tags | grep gpu)
          echo "paths=$paths" >> $GITHUB_ENV
        env:
          paths: ${{ steps.list.outputs.paths }}

  nf-test-gpu:
    runs-on: "gpu"
    name: "GPU | ${{ matrix.profile }} | ${{ matrix.shard }}"
    needs: nf-test-changes
    if: ${{ needs.nf-test-changes.outputs.components != '[]' }}
    strategy:
      fail-fast: false
      matrix:
        NXF_VER:
          - "24.04.2"
          - "latest-everything"
        shard: [1, 2]
        filter: [pipeline, workflow]
        profile:
          - "docker"
          - "singularity"
        isMaster:
          - ${{ github.base_ref == 'master' }}
        # Exclude conda and singularity on dev
        exclude:
          - isMaster: false
            profile: "conda"
          - isMaster: false
            profile: "singularity"
    env:
      NXF_ANSI_LOG: false
      TOTAL_SHARDS: 2

    steps:
      - name: Check out pipeline code
        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
        with:
          fetch-depth: 0

      - name: Set up Nextflow
        uses: nf-core/setup-nextflow@v2
        with:
          version: "${{ matrix.NXF_VER }}"

      - name: Install pdiff to see diff between nf-test snapshots
        run: |
          python -m pip install --upgrade pip
          pip install pdiff

      - uses: nf-core/setup-nf-test@v1
        with:
          version: ${{ env.NFT_VER }}

      - name: Set up Apptainer
        if: matrix.profile == 'singularity'
        uses: eWaterCycle/setup-apptainer@main

      - name: Set up Singularity
        if: matrix.profile == 'singularity'
        run: |
          mkdir -p $NXF_SINGULARITY_CACHEDIR
          mkdir -p $NXF_SINGULARITY_LIBRARYDIR

      - name: Clean up Disk space
        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1

      - name: Run GPU Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }})
        run: |
          nf-test test \
              --ci \
              --shard ${{ matrix.shard }}/${{ strategy.job-total }} \
              --changed-since HEAD^ \
              --profile "+${{ matrix.profile }}" \
              --filter ${{ matrix.filter }} \
              --tag "gpu"

      - name: Output log on failure
        if: failure()
        run: |
          sudo apt install bat > /dev/null
          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log

      - name: Publish Test Report
        uses: mikepenz/action-junit-report@v3
        if: always() # always run even if the previous step fails
        with:
          report_paths: test.xml

  nf-test:
    name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.profile }})"
    # Only run on push if this is the nf-core dev branch (merged PRs)
    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/methylseq') }}"
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        NXF_VER:
          - "24.04.2"
          - "latest-everything"
        shard: [1, 2, 3, 4, 5]
        filter: [pipeline, workflow]
        profile:
          - "conda"
          - "docker"
          - "singularity"
        isMaster:
          - ${{ github.base_ref == 'master' }}
        # Exclude conda and singularity on dev
        exclude:
          - isMaster: false
            profile: "conda"
          - isMaster: false
            profile: "singularity"
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
        with:
          fetch-depth: 0

      - name: Set up Nextflow
        uses: nf-core/setup-nextflow@v2
        with:
          version: "${{ matrix.NXF_VER }}"

      - name: Install pdiff to see diff between nf-test snapshots
        run: |
          python -m pip install --upgrade pip
          pip install pdiff

      - uses: nf-core/setup-nf-test@v1
        with:
          version: ${{ env.NFT_VER }}

      - name: Set up Apptainer
        if: matrix.profile == 'singularity'
        uses: eWaterCycle/setup-apptainer@main

      - name: Set up Singularity
        if: matrix.profile == 'singularity'
        run: |
          mkdir -p $NXF_SINGULARITY_CACHEDIR
          mkdir -p $NXF_SINGULARITY_LIBRARYDIR

      - name: Set up Miniconda
        if: matrix.profile == 'conda'
        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
        with:
          miniconda-version: "latest"
          auto-update-conda: true
          conda-solver: libmamba
          channels: conda-forge,bioconda

      - name: Set up Conda
        if: matrix.profile == 'conda'
        run: |
          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
          echo $(realpath python) >> $GITHUB_PATH

      - name: Clean up Disk space
        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1

      - name: Run Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }})
        run: |
          nf-test test \
              --ci \
              --shard ${{ matrix.shard }}/${{ strategy.job-total }} \
              --changed-since HEAD^ \
              --profile "+${{ matrix.profile }}" \
              --filter ${{ matrix.filter }}

      - name: Output log on failure
        if: failure()
        run: |
          sudo apt install bat > /dev/null
          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log

      - name: Publish Test Report
        uses: mikepenz/action-junit-report@v3
        if: always() # always run even if the previous step fails
        with:
          report_paths: test.xml