Convert Workflow Definition Language (WDL) to CWL
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tetron Merge pull request #5 from wtsi-hgi/4-command-continuation-fix
Removes continuation whitespace from wdl command
Latest commit c9aff7c Jun 16, 2017

README.md

Converter from the Broad Institute's Workflow Definition Language (WDL) to the Common Workflow Language.

Generates a set of CWL files from a WDL workflow which can be executed with a CWL implementation.

Installation

git clone https://github.com/common-workflow-language/wdl2cwl.git
cd wdl2cwl
python setup.py install

PyPi package coming soon

Usage:

Pass a wdl workflow or a directory with wdl files to wdl2cwl

wdl2cwl <workflow.wdl> | <directory> [options]

By default, a directory with a name of the wdl file will be created and all generated CWL files will be placed in that directory.

Additional options

'-d', '--directory' - Target directory to place CWL files

'-q', '--quiet' - Do not print generated tools to stdout

--no-folder - Do not create a separate folder for each CWL toolset (convenient whilst bulk conversion of standalone tools, not workflows)

Notes on autoconverting

Not every WDL workflow can be automatically mapped to CWL. Sometimes some additional tweaks after CWL generation are required:

Secondary files

If any of the input parameters include files that must be processed together, they should be mentioned in secondaryFiles field:

secondaryFiles
- .fai
- ^.dict

Runtime (WDL)

docker [] -> DockerRequirement, only one image

resources -> ResourceRequirement, megabytes -> mebibytes string

Outputs

If the output {...} section is omitted in WDL, then the CWL workflow includes all outputs from all calls in its final output.

WDL standard library functions

Not all WDL functions are covered.

Some of WDL functions can be effectively replaced by a CWL expression. For instance, if you need to get the basename of a file, sub - effectively replaced by inputs.path.basename

read_X() functions:

if an input parameter is read from a file by a function like read_tsv or read_csv, it must start with a backslash. wdl2cwl has to transform file inputs in plain strings to a CWL File object. wdl2cwl only recognizes a filepath in a .txt file if it starts with a backslash. Moreover, all strings starting with '/' will be treated as filepathes.

Resource and docker requirements:

Resource requirements in WDL are set in megabytes vs mebibytes in CWL

References:

CWL spec https://github.com/common-workflow-language/common-workflow-language

WDL spec https://github.com/broadinstitute/wdl

Python WDL parser https://github.com/broadinstitute/pywdl

cwl2wdl (convert the other way) https://github.com/adamstruck/cwl2wdl