Common workflow language tool description reference implementation

This is the reference implementation of the Common Workflow Language. It is intended to be feature complete and provide comprehensive validation of CWL files as well as provide other tools related to working with CWL.

This is written and tested for Python 2.7.

The reference implementation consists of two packages. The "cwltool" package is the primary Python module containing the reference implementation in the "cwltool" module and console executable by the same name.

The "cwl-runner" package is optional and provides an additional entry point under the alias "cwl-runner", which is the implementation-agnostic name for the default CWL interpreter installed on a host.

Install

Installing the official package from PyPi (will install "cwltool" package as well):

pip install cwl-runner

Or from source:

git clone https://github.com/common-workflow-language/cwltool.git
cd cwltool && python setup.py install
cd cwl-runner && python setup.py install

Run on the command line

Simple command:

cwl-runner [tool] [job]

Import as a module

Add:

import cwltool

to your script.

Use with boot2docker

boot2docker is running docker inside a virtual machine and it only mounts Users on it. The default behavoir of CWL is to create temporary directories under e.g. /Var which is not accessible to Docker containers.

To run CWL successfully with boot2docker you need to set the --tmpdir-prefix and --tmp-outdir-prefix to somewhere under /Users:

$ cwl-runner --tmp-outdir-prefix=/Users/username/project --tmpdir-prefix=/Users/username/project wc-tool.cwl wc-job.json