name: bowtie2_align
on:
    push:
        paths:
            - software/bowtie2/align/**
            - software/bowtie2/build/**
            - .github/workflows/bowtie2_align.yml
            - tests/software/bowtie2/**
    pull_request:
        paths:
            - software/bowtie2/align/**
            - software/bowtie2/build/**
            - .github/workflows/bowtie2_align.yml
            - tests/software/bowtie2/**

jobs:
    ci_test:
        runs-on: ubuntu-latest
        strategy:
            matrix:
                nxf_version: [20.11.0-edge]
        env:
            NXF_ANSI_LOG: false
        steps:
            - uses: actions/checkout@v2

            - name: Install Nextflow
              env:
                  NXF_VER: ${{ matrix.nxf_version }}
              run: |
                  wget -qO- get.nextflow.io | bash
                  sudo mv nextflow /usr/local/bin/

            - name: Set up Python
              uses: actions/setup-python@v2
              with:
                  python-version: "3.x"
            - name: Install dependencies
              run: python -m pip install --upgrade pip pytest-workflow

            # Test the module
            - run: pytest --tag bowtie2_align --symlink --wt 2