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Convertion from WDL workflow descriptions to CWL

Project Description

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

Generates a directory with a set of CWL files which can be executed with a CWL implementation.

Usage: wdl2cwl workflow.wdl

## 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

#### Runtime (WDL) docker [] -> DockerRequirement, only one image resources -> ResourceRequirement, megabytes -> mebibytes string

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

На вході у ворклоф немає параметра, він передається імпліцитно через інпут файл

sub - effectively replaced by inputs.path.basename

secondaryFiles - .fai - ^.dict

step level variables: if several variables with the same name declared - works in WDL, doesn’t work in CWL

resource and docker requirements: megabytes vs mebibytes

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.

## 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

Release History

Release History

This version
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0.2.1

History Node

0.2

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wdl2cwl-0.2.1.tar.gz (9.3 kB) Copy SHA256 Checksum SHA256 Source Feb 21, 2017

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