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 (AMP and ARG workflows)
    # 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/funcscan') }}"
    runs-on: ubuntu-latest
    strategy:
      matrix:
        NXF_VER:
          - "23.04.0"
          - "latest-everything"
        parameters:
          - "--annotation_tool prodigal"
          - "--annotation_tool prokka"
          - "--annotation_tool bakta --annotation_bakta_db_downloadtype light"

    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 (AMP and ARG workflows)
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}

  test_bgc:
    name: Run pipeline with test data (BGC workflow)
    # 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/funcscan') }}"
    runs-on: ubuntu-latest
    strategy:
      matrix:
        NXF_VER:
          - "23.04.0"
          - "latest-everything"
        parameters:
          - "--annotation_tool prodigal"
          - "--annotation_tool prokka"
          - "--annotation_tool bakta --annotation_bakta_db_downloadtype light"

    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: Run pipeline with test data (BGC workflow)
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile test_bgc,docker --outdir ./results ${{ matrix.parameters }}

  test_deeparg:
    name: Run pipeline with test data (DeepARG only workflow)
    # 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/funcscan') }}"
    runs-on: ubuntu-latest
    strategy:
      matrix:
        NXF_VER:
          - "23.04.0"
          - "latest-everything"
        parameters:
          - "--annotation_tool bakta --annotation_bakta_db_downloadtype light"
          - "--annotation_tool pyrodigal"

    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: Run pipeline with test data (DeepARG workflow)
        run: |
          wget https://zenodo.org/record/8280582/files/deeparg.zip ## download from zenodo due to instability of deepARG server
          unzip deeparg.zip
          nextflow run ${GITHUB_WORKSPACE} -profile test_deeparg,docker --outdir ./results ${{ matrix.parameters }} --arg_deeparg_data 'deeparg/'