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Common workflow language tool description reference implementation

CWL Conformance test: Build Status

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 "cwlref-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 cwlref-runner

If installling alongside another CWL implementation then:

pip install cwltool

To install from source:

git clone https://github.com/common-workflow-language/cwltool.git
cd cwltool && python setup.py install
cd cwlref-runner && python setup.py install  # co-installing? skip this

Remember, if co-installing multiple CWL implementations then you need to maintain which implementation cwl-runner points to via a symbolic file system link or [another facility](https://wiki.debian.org/DebianAlternatives).

Run on the command line

Simple command:

cwl-runner [tool-or-workflow-description] [input-job-settings]

Or if you have multiple CWL implementations installed and you want to override the default cwl-runner use:

cwltool [tool-or-workflow-description] [input-job-settings]

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

Tool or workflow loading from remote or local locations

cwltool can run tool and workflow descriptions on both local and remote systems via its support for HTTP[S] URLs.

Input job files and Workflow steps (via the run directive) can reference CWL documents using absolute or relative local filesytem paths. If a relative path is referenced and that document isn't found in the current directory then the following locations will be searched: http://www.commonwl.org/v1.0/CommandLineTool.html#Discovering_CWL_documents_on_a_local_filesystem

Use with GA4GH Tool Registry API

Cwltool can launch tools directly from GA4GH Tool Registry API endpoints.

By default, cwltool searches https://dockstore.org/ . Use --add-tool-registry to add other registries to the search path.

For example

cwltool --non-strict quay.io/collaboratory/dockstore-tool-bamstats:master test.json

and (defaults to latest when a version is not specified)

cwltool --non-strict quay.io/collaboratory/dockstore-tool-bamstats test.json

For this example, grab the test.json (and input file) from https://github.com/CancerCollaboratory/dockstore-tool-bamstats