.travis.yml

language: python
python: 3.7

install:
  # conda env
  - wget "https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh" -O miniconda.sh
  - bash miniconda.sh -b -p $HOME/miniconda
  - source "$HOME/miniconda/etc/profile.d/conda.sh"
  - hash -r
  - conda config --set always_yes yes --set changeps1 no
  - conda info -a
  # pipeline env
  - conda env create -f cwl/requirements/conda_env.yml
  - conda activate viral_pipeline

script:
  # CWL validation
  - cwltool --enable-dev --validate $TRAVIS_BUILD_DIR/cwl/src/pipeline.cwl
  # CWL tests
  - cd $TRAVIS_BUILD_DIR/cwl/tests
  # NOTE: run only tests that do not require DBs or files from the FTP server
  - bash cwltest.sh --test tests.yml -j 4 --verbose -n 1,4,5,6,10,11,12,13,14,20
  # Python tests
  - cd $TRAVIS_BUILD_DIR/
  - python -m unittest discover tests

cache: pip