ci.yml

name: CI

on:
  push:
    branches:
      - master
  pull_request:
    branches:
      - master

jobs:
  build:
    runs-on: ubuntu-20.04

    strategy:
      matrix:
        include:
          - name: Variant standard
            env:
              BCBIO_DOCKER_PRIVILEGED: True
              ARVADOS_API_HOST: qr1hi.arvadosapi.com

          - name: Variant CWL

          - name: RNA-seq CWL

    env:
      ANACONDA_INSTALL_DIR: ~/install/bcbio-vm/anaconda

    steps:
      - name: Check if only Markdown files changed
        run: |
          if ! git diff --name-only ${{ github.event.before }}..${{ github.sha }} | grep -qvE '(.md)'
          then
            echo "Not running CI since only docs were changed"
            exit 0
          fi

      - name: Update packages and install Miniconda
        run: |
          sudo apt update
          wget --progress=dot:giga https://repo.anaconda.com/miniconda/Miniconda3-py37_4.8.2-Linux-x86_64.sh
          bash Miniconda3-py37_4.8.2-Linux-x86_64.sh -b -p ${{ env.ANACONDA_INSTALL_DIR }}

      - name: Install bcbio-nextgen and bcbio-nextgen-vm
        run: |
          export PATH=${{ env.ANACONDA_INSTALL_DIR }}/bin:$PATH
          conda install --yes nomkl
          conda install --yes -c conda-forge -c bioconda bcbio-nextgen python=3
          conda install --yes -c conda-forge -c bioconda bcbio-nextgen-vm python=3
          conda clean --yes --tarballs --index-cache
          rm -rf ${{ env.ANACONDA_INSTALL_DIR }}/pkgs/qt-*
          du -sch ${{ env.ANACONDA_INSTALL_DIR }}/pkgs/* | sort -h

      - name: Update bcbio-nextgen code
        run: |
          rm -rf ${{ env.ANACONDA_INSTALL_DIR }}/lib/python*/site-packages/bcbio
          rm -rf ${{ env.ANACONDA_INSTALL_DIR }}/lib/python*/site-packages/bcbio_nextgen-*
          ${{ env.ANACONDA_INSTALL_DIR }}/bin/python setup.py install

      - name: Variant tests
        if: matrix.name == 'Variant standard' || matrix.name == 'Variant CWL'
        run: |
          docker pull quay.io/bcbio/bcbio-vc
          docker images
          bcbio_vm.py devel setup_install -i quay.io/bcbio/bcbio-vc
          py.test -p no:cacheprovider -p no:stepwise tests/bcbio_vm -v -s
          docker ps -a -q | xargs --no-run-if-empty docker rm
          docker rmi -f quay.io/bcbio/bcbio-vc
          docker images | grep '<none>' | awk '{print $3}' | xargs --no-run-if-empty docker rmi

      - name: RNA-seq tests
        if: matrix.name == 'RNA-seq CWL'
        run: |
          docker pull quay.io/bcbio/bcbio-rnaseq
          docker images
          bcbio_vm.py devel setup_install -i quay.io/bcbio/bcbio-rnaseq
          py.test -p no:cacheprovider -p no:stepwise tests/bcbio_vm -v -s
          docker ps -a -q | xargs --no-run-if-empty docker rm
          docker rmi -f quay.io/bcbio/bcbio-rnaseq
          docker images | grep '<none>' | awk '{print $3}' | xargs --no-run-if-empty docker rmi

      - name: Cleanup
        run: df -h

      - name: Notify on failure
        if: failure()
        run: echo "Build failed"