2.1

• Fix generated expressions, where a parameter is not a valid javascript name
• Remove console.log and incorrect comments from the javascript library
• Generate gatk version 4.0.0.0

2.0

• Added no_docker and use_cache command line option
• Fixed beheviour of array and tag types
• Rewrote gen_cwl_arg to be clearer
• Reduced the dependance on the command line for the tests

Breaking changes:

• Removed the refIndex, refDict and analysis_type cwl parameters
• Changed docker_container_name to docker_image_name

1.4.2

Use full GATK versions in release paths (i.e. "3.8-0" instead of just "3-8") and refer to specific version of latest GATK 4 beta release ("4.beta.6" rather than "latest").

v1.4.1

Add releases in .tgz and .tar.bz2 archive formats. Add gatk-cwl-generator version to release filenames.

v1.4.0

Changes generated CWL to YAML format rather than JSON for improved readability.

v1.3

• Changed the docker container to be broad institute's official docker container, not wtsi-hgi own container

v1.2.2

• Resolving secondaryFiles to a relative path, to work with newer cwl-runner versions and the advice in "secondaryFiles" of http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter

v1.2.1

Changes:

• Array types are type | type[]

v1.1

Changes:

• Made output arguments's ids be Output instead of adding dashes
• Outputting to gatk_cmdline_tools

v1.0

Includes CWL files for GATK 3.5 - 3.8