CWL documents describe workflows made of command line data analysis tools in a portable, reproducible, and reusable fashion.

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common-workflow-language / common-workflow-language

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Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊

science workflow containers common-workflow-language cwl workflows commonwl sciworkflows

• Updated Nov 13, 2020
• Python

broadinstitute / cromwell

Star 624

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

docker application workflow cloud bioinformatics scala executor hpc containers wdl common-workflow-language ga4gh cwl workflow-description-language workflow-execution

• Updated Dec 19, 2020
• Scala

common-workflow-language / cwltool

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Open

--validate on a $graph CWL document should validate all objects without prompting

mr-c commented Oct 31, 2020

Expected Behavior

cwltool --validate https://github.com/common-workflow-language/cwl-v1.2/raw/main/tests/conflict-wf.cwl validates all objects inthe file.

Actual Behavior

Tell us what happens instead

INFO /usr/bin/cwltool 3.0.20200807132242
ERROR Tool definition failed initialization:
Tool file contains graph of multiple objects, must specify one of #echo, #cat, #collision

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good first issue help wanted

Open

"paths starting with '/' only permitted in CWL 1.2 and later" error message needs to be more helpful

6

Open

Clarify if --preserve-environment works with docker/Singularity

4

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CBICA / CaPTk

Star 91

Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk/

machine-learning analytics cpp cancer cpp11 medical-imaging cancer-imaging-research image-analysis medical-image-computing cwl itcr radiomics medical-image-processing nih nci nci-itcr radiomics-features cwltool u24 cbica

• Updated Dec 18, 2020
• C++

rabix / benten

Star 36

A language server for Common Workflow Language

editor workflow language-server ide common-workflow-language cwl cwl-documents

• Updated Dec 18, 2020
• Python

common-workflow-language / cwlviewer

Star 25

A web application to view and share Common Workflow Language workflows

workflow common-workflow-language cwl workflows

• Updated Dec 15, 2020
• Java

Created by Peter Amstutz, John Chilton, Michael R. Crusoe, Nebojša Tijanić, and the CWL Community

Released January 2015

Organization

common-workflow-language

Website

www.commonwl.org

Wikipedia

Wikipedia