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/epitopeprediction') }}"
    runs-on: ubuntu-latest
    strategy:
      matrix:
        NXF_VER:
          - "22.10.1"
          - "latest-everything"
    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
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
  profile:
    name: Run profile tests
    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/epitopeprediction') }}
    runs-on: ubuntu-latest
    env:
      NXF_VER: ${{ matrix.nxf_ver }}
      NXF_ANSI_LOG: false
    strategy:
      matrix:
        include:
          # Test pipeline minimum Nextflow version
          - NXF_VER: "22.10.1"
            NXF_EDGE: ""
          # Test latest edge release of Nextflow
          - NXF_VER: ""
            NXF_EDGE: "1"
        tests:
          [
            "test_variant_tsv",
            "test_grch38_variant_tsv",
            "test_peptides",
            "test_peptides_h2",
            "test_proteins",
            "test_mhcnuggets",
            "test_mhcflurry",
          ]
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v2
      - name: Install Nextflow
        env:
          NXF_VER: ${{ matrix.NXF_VER }}
          # Uncomment only if the edge release is more recent than the latest stable release
          # See https://github.com/nextflow-io/nextflow/issues/2467
          # NXF_EDGE: ${{ matrix.NXF_EDGE }}
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/
      - name: Run pipeline with profile ${{ matrix.tests }}
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.tests }},docker --outdir ./results

  nonfree:
    name: Run NetMHC tool family tests
    if: ${{ ( github.event_name == 'push' && github.repository == 'nf-core/epitopeprediction' ) || github.event.pull_request.head.repo.full_name == 'nf-core/epitopeprediction' }}
    runs-on: ubuntu-latest
    env:
      NXF_VER: ${{ matrix.nxf_ver }}
    strategy:
      matrix:
        include:
          # Test pipeline minimum Nextflow version
          - NXF_VER: "22.10.1"
            NXF_EDGE: ""
          # Test latest edge release of Nextflow
          - NXF_VER: ""
            NXF_EDGE: "1"
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v2

      - name: Install non-free software
        env:
          DECRYPT_PASSPHRASE: ${{ secrets.TEST_NETMHC }}
        run: |
          mkdir -v non-free
          curl -L https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/software/non-free-software.tar.gpg | ${GITHUB_WORKSPACE}/bin/decrypt | tar -C non-free -v -x

      - name: Install Nextflow
        env:
          NXF_VER: ${{ matrix.NXF_VER }}
          # Uncomment only if the edge release is more recent than the latest stable release
          # See https://github.com/nextflow-io/nextflow/issues/2467
          # NXF_EDGE: ${{ matrix.NXF_EDGE }}
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/
      - name: Run pipeline with NetMHC
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile test_netmhc,docker --outdir ./results
      - name: Run pipeline with NetMHCpan
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile test_netmhcpan,docker --outdir ./results
