Python classes for loading, manipulating CWL documents

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.

Modules

Contents:

API Reference
- cwl_utils

Included Utility Programs

cwl-cite-extract

Print information about software used in a CWL document (Workflow or CommandLineTool). For CWL Workflows, all steps will also be searched (recursively).

usage: cwl-cite-extract [-h] input

input: Input CWL document (CWL Workflow or CWL CommandLineTool)

-h, --help: show this help message and exit

cwl-docker-extract

Save container images specified in a CWL document (Workflow or CommandLineTool). For CWL Workflows, all steps will also be searched (recursively).

usage: cwl-docker-extract [-h] [--dir DIR] [-s]
                          [--container-engine CONTAINER_ENGINE]
                          [--force-download]
                          input

input: Input CWL document (CWL Workflow or CWL CommandLineTool)

-h, --help: show this help message and exit

--dir <dir>: Directory in which to save images

-s, --singularity: Use singularity to pull the image

--container-engine <container_engine>: Specify which command to use to run OCI containers. Defaults to ‘docker’ (or ‘singularity’ if –singularity/-s is passed).

--force-download: Force pulling a newer container.

cwl-expression-refactor

Tool to refactor CWL documents so that any CWL expression are separate steps as either ExpressionTools or CommandLineTools. Exit code 7 means a single CWL document was provided but it did not need modification.

usage: cwl-expression-refactor [-h] [--etools] [--skip-some1] [--skip-some2]
                               dir inputs [inputs ...]

dir: Directory in which to save converted files

inputs: One or more CWL documents.

-h, --help: show this help message and exit

--etools: Output ExpressionTools, don’t go all the way to CommandLineTools.

--skip-some1: Don’t process CommandLineTool.inputs.inputBinding and CommandLineTool.arguments sections.

--skip-some2: Don’t process CommandLineTool.outputEval or CommandLineTool.requirements.InitialWorkDirRequirement.

cwl-graph-split

Split a packed CWL document.

usage: cwl-graph-split [-h] [-m MAINFILE] [-f {json,yaml}] [-p] [-C OUTDIR]
                       cwlfile

cwlfile

-h, --help: show this help message and exit

-m <mainfile>, --mainfile <mainfile>: Specify the name of the main document.

-f {json,yaml}, --output-format {json,yaml}: Specify the format of the output CWL files.

-p, --pretty: Beautify the output CWL document, only works with yaml format.

-C <outdir>, --outdir <outdir>: Output folder for the unpacked CWL files.

cwl-normalizer

Normalizes CWL documents. Will upgrade to CWL v1.2, and pack the result. Can optionally refactor out CWL expressions.

usage: cwl-normalizer [-h] [--etools] [--skip-some1] [--skip-some2]
                      [--no-expression-refactoring]
                      dir inputs [inputs ...]

dir: Directory in which to save converted files

inputs: One or more CWL documents.

-h, --help: show this help message and exit

--etools: Output ExpressionTools, don’t go all the way to CommandLineTools.

--skip-some1: Don’t process CommandLineTool.inputs.inputBinding and CommandLineTool.arguments sections.

--skip-some2: Don’t process CommandLineTool.outputEval or CommandLineTool.requirements.InitialWorkDirRequirement.

--no-expression-refactoring: Don’t do any CWL expression refactoring.