Test code for bcbio CWL support

A self-contained test environment for running Common Workflow Language (CWL) inputs on multiple CWL supporting platforms. Uses bcbio's CWL support to generate and run CWL, see the CWL documentation for detailed instructions about installing bcbio and running workflows.

Test cases

• somatic -- Tumor/normal like samples, with multiple aligners and variantcallers. This has work in progress attempts to convert to WDL and Nextflow.
• gvcf_joint -- Germline joint calling using gVCF intermediates.
• svcall -- Structural variant calling.
• arvados -- Test integration upload and runs on Arvados.

Requirements

If you have a working setup on your local machine and use Docker, this test directory requires no extra installations. All of the necessary data is available in this repository, the CWL files are pre-built, and you don't need an external bcbio installation.

Alternative bcbio provides wrapper scripts if you don't have CWL tools installed, lack experience running them, want to regenerate the CWL from bcbio YAML files, or can't use Docker. To install the wrapper scripts, and optionally bcbio tools:

• Install bcbio-vm -- this installs bcbio_vm.py with wrappers for generating and running CWL, as well as the common CWL runners we use (Toil, Rabix bunny, cwltool).

• Install a full version of bcbio_nextgen.py with tools. If you're using Docker these test runs pull in bcbio Docker containers directly and you don't need to do anything. If you're not using Docker, you need a separate installation of bcbio and tools available on your PATH. If you're only using this for testing you can install bcbio with --nodata since the tests are not dependent on external data.

Running

• Change into a test directory:

    cd somatic
  

• Optionally, re-generate the CWL. This is generally not needed unless you explicitly want to test CWL generation:

    bash run_generate_cwl.sh
  

• Run a test case, you'll likely have to edit the run_$TOOL.sh scripts to match the type of environment you want to run in (Docker, local, cluster):

    bash run_toil.sh
  

  These scripts use bcbio wrappers around the CWL running tools. You can also run the tools directly without any wrappers.

License

All CWL workflows, scripts and documentation are freely available for all uses under the MIT license.