.travis.yml

os: linux
dist: bionic
language: generic

before_install:
  - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
  - bash Miniconda3-latest-Linux-x86_64.sh -b -p ~/bcbio-vm/anaconda
  - export PATH=~/bcbio-vm/anaconda/bin:$PATH

install: conda install --yes -c conda-forge -c bioconda bcbio-nextgen bcbio-nextgen-vm

jobs:
  include:
    # pull Docker images in before_script and disable stdout capture in tests to prevent output timeout errors
    - script: pytest -s -v tests/test_docker.py
      name: "Variant standard"
      before_script: docker pull quay.io/bcbio/bcbio-vc
    - script: pytest -s -v tests/test_cwl.py::test_cwl_docker_somatic_workflow
      name: "Variant CWL"
      before_script: docker pull quay.io/bcbio/bcbio-vc
    - script: pytest -s -v tests/test_cwl.py::test_cwl_local_somatic_workflow
      name: "Variant CWL local"
      before_script: docker pull quay.io/bcbio/bcbio-vc
    - script: pytest -s -v tests/test_cwl.py::test_cwl_rnaseq
      name: "RNA-seq CWL"
      before_script: docker pull quay.io/bcbio/bcbio-rnaseq