taxprofiler/.github/workflows/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]

env:
  NXF_ANSI_LOG: false

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

jobs:
  test:
    name: Run pipeline with test data
    # 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/taxprofiler') }}"
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        NXF_VER:
          - "22.10.1"
          - "latest-everything"
        parameters:
          - "--preprocessing_qc_tool falco"
          - "--perform_longread_qc false"
          - "--perform_shortread_qc false"
          - "--shortread_qc_tool fastp"
          - "--shortread_qc_tool fastp --shortread_qc_mergepairs --shortread_qc_includeunmerged"
          - "--shortread_qc_tool fastp --shortread_qc_mergepairs"
          - "--shortread_qc_tool adapterremoval"
          - "--shortread_qc_tool adapterremoval --shortread_qc_mergepairs --shortread_qc_includeunmerged"
          - "--shortread_qc_tool adapterremoval --shortread_qc_mergepairs"
          - "--shortread_complexityfilter_tool bbduk"
          - "--shortread_complexityfilter_tool prinseqplusplus"
          - "--perform_runmerging"
          - "--perform_runmerging --shortread_qc_mergepairs"
          - "--shortread_complexityfilter false --perform_shortread_hostremoval"

    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: Show current locale
        run: locale

      - name: Set UTF-8 enabled locale
        run: |
          sudo locale-gen en_US.UTF-8
          sudo update-locale LANG=en_US.UTF-8          

      - name: Run pipeline with test data
        uses: Wandalen/wretry.action@v1.0.11
        with:
          command: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
          attempt_limit: 3

  motus:
    name: Test mOTUs with workflow parameters
    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}
    runs-on: ubuntu-latest
    strategy:
      matrix:
        NXF_VER:
          - "22.10.1"
          - "latest-everything"

    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v2

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

      - name: Show current locale
        run: locale

      - name: Set UTF-8 enabled locale
        run: |
          sudo locale-gen en_US.UTF-8
          sudo update-locale LANG=en_US.UTF-8          

      - name: Prepare the database
        run: |
          wget https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py
          python downloadDB.py > download_db_log.txt
          echo 'tool,db_name,db_params,db_path' > 'database_motus.csv'
          echo 'motus,db_mOTU,,db_mOTU' >> 'database_motus.csv'          

      - name: Run pipeline with test data
        uses: Wandalen/wretry.action@v1.0.11
        with:
          command: nextflow run ${GITHUB_WORKSPACE} -profile test_motus,docker --outdir ./results --databases ./database_motus.csv
          attempt_limit: 3

  krakenuniq:
    name: Test KrakenUniq with workflow parameters
    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}
    runs-on: ubuntu-latest
    strategy:
      matrix:
        NXF_VER:
          - "22.10.1"
          - "latest-everything"

    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v2

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

      - name: Show current locale
        run: locale

      - name: Set UTF-8 enabled locale
        run: |
          sudo locale-gen en_US.UTF-8
          sudo update-locale LANG=en_US.UTF-8          

      - name: Run pipeline with test data
        uses: Wandalen/wretry.action@v1.0.11
        with:
          command: nextflow run ${GITHUB_WORKSPACE} -profile test_krakenuniq,docker --outdir ./results
          attempt_limit: 3

  malt:
    name: Test MALT with workflow parameters
    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}
    runs-on: ubuntu-latest
    strategy:
      matrix:
        NXF_VER:
          - "22.10.1"
          - "latest-everything"

    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v2

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

      - name: Show current locale
        run: locale

      - name: Set UTF-8 enabled locale
        run: |
          sudo locale-gen en_US.UTF-8
          sudo update-locale LANG=en_US.UTF-8          

      - name: Run pipeline with test data
        uses: Wandalen/wretry.action@v1.0.11
        with:
          command: nextflow run ${GITHUB_WORKSPACE} -profile test_nothing,docker --run_malt --input 'https://github.com/nf-core/test-datasets/raw/taxprofiler/samplesheet_shortreadsonly.csv' --outdir ./results
          attempt_limit: 3