Common Workflow Language
CWL documents describe workflows made of command line data analysis tools in a portable, reproducible, and reusable fashion.
- GitHub: https://github.com/topics/cwl
- Wikipedia: https://en.wikipedia.org/wiki/Common_Workflow_Language
- Repo: https://github.com/common-workflow-language
- Created by: Peter Amstutz, John Chilton, Michael R. Crusoe, Nebojša Tijanić, and the CWL Community
- Released: January 2015
- Aliases: common-workflow-language, commonwl,
- Last updated: 2026-02-28 00:07:19 UTC
- JSON Representation
https://github.com/common-workflow-language/common-workflow-language
Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊
common-workflow-language commonwl containers cwl science sciworkflows workflow workflows
Last synced: 13 May 2025
https://github.com/databiosphere/toil
A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.
aws common-workflow-language cwl gridengine kubernetes mesos pipeline python slurm wdl workflow workflow-description-language
Last synced: 29 Apr 2025
https://github.com/DataBiosphere/toil
A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.
aws common-workflow-language cwl gridengine kubernetes mesos pipeline python slurm wdl workflow workflow-description-language
Last synced: 07 Apr 2025
https://github.com/common-workflow-language/cwltool
Common Workflow Language reference implementation
common-workflow-language commonwl containers cwl science sciworkflows workflows
Last synced: 08 Jan 2026
https://github.com/rabix/composer
Visual and code editor for Common Workflow Language
common-workflow-language cwl editor ide
Last synced: 18 Jan 2026
https://github.com/Barski-lab/cwl-airflow
Python package to extend Airflow functionality with CWL1.1 support
common-workflow-language commonwl containers cwl cwl-airflow cwl-descriptor dag workflow
Last synced: 18 Jul 2025
https://github.com/CBICA/CaPTk
Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk
analytics cancer cancer-imaging-research cbica cpp cpp11 cwl cwltool image-analysis itcr machine-learning medical-image-computing medical-image-processing medical-imaging nci nci-itcr nih radiomics radiomics-features u24
Last synced: 07 May 2025
https://github.com/dockstore/dockstore
An app store for scientific workflows, tools, notebooks, and services
bioinformatics containers cwl docker dockstore nextflow wdl workflow
Last synced: 20 Jan 2026
https://github.com/ga4gh/workflow-execution-service-schemas
The WES API is a standard way to run and manage portable workflows.
Last synced: 23 Jan 2026
https://github.com/rabix/cwl-svg
A library for generating an interactive SVG visualization of CWL workflows
bioinformatics cwl svg visualization workflow
Last synced: 17 Jan 2026
https://github.com/4dn-dcic/tibanna
Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.
aws aws-lambda aws-step-function bioinformatics conda cwl cwl-workflow docker ot2od032119 pipelines snakemake snakemake-workflow u01ca200059 wdl wdl-workflow
Last synced: 18 Jan 2026
https://github.com/rabix/cwl-ts
Typescript data model for Common Workflow Language
common-workflow-language cwl typescript workflow
Last synced: 18 Jan 2026
https://github.com/common-workflow-language/cwlviewer
A web application to view and share Common Workflow Language workflows
common-workflow-language cwl java workflow workflows
Last synced: 02 Sep 2025
https://github.com/common-workflow-language/user_guide
The CWL v1.0 - v1.2 user guide
common-workflow-language cwl workflow workflows
Last synced: 03 Feb 2026
https://github.com/Duke-GCB/calrissian
CWL on Kubernetes
cwl cwl-workflow cwl-workflows kubernetes
Last synced: 10 Mar 2025
https://github.com/NLeSC/scriptcwl
Create cwl workflows by writing a simple Python script
Last synced: 10 Mar 2025
https://github.com/nlesc/scriptcwl
Create cwl workflows by writing a simple Python script
Last synced: 17 Jun 2025
https://github.com/stjudecloud/workflows
Bioinformatics workflows developed for and used on the St. Jude Cloud project.
bioinformatics bioinformatics-workflows computational-biology cromwell cwl cwl-workflow genomics next-generation-sequencing stjudecloud wdl wdl-workflow workflow workflow-engine workflows
Last synced: 19 Feb 2026
https://github.com/common-workflow-language/cwl-utils
Python utilities for CWL
common-workflow-language commonwl cwl
Last synced: 04 Apr 2025
https://github.com/nlppln/nlppln
NLP pipeline software using common workflow language
cwl nlp pipeline text-mining workflow
Last synced: 10 Mar 2025
https://github.com/yyoshiaki/VIRTUS
A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.
Last synced: 10 Mar 2025
https://github.com/otiai10/hotsub
Command line tool to run batch jobs concurrently with ETL framework on AWS or other cloud computing resources
aws batch-job bioinformatics cwl cwl-workflow docker docker-machine etl-framework gcp wdl wdl-workflow workflow workflow-engine
Last synced: 16 Oct 2025
https://github.com/crim-ca/weaver
Weaver: Workflow Execution Management Service (EMS); Application, Deployment and Execution Service (ADES); OGC API - Processes; WPS; CWL Application Package
ades common-workflow-language cwl ems ogc ogc-api-processes remote-execution web-application web-processing-service workflow wps
Last synced: 16 Jan 2026
https://github.com/common-workflow-lab/wdl-cwl-translator
A translator from WDL to CWL v1.2
Last synced: 02 Feb 2026
https://github.com/daylily-informatics/daylily
A NGS analysis framework for WGS data, which automates the entire process of spinning up AWS EC2 spot instances and processing FASTQ to snvVCF in <60m, for dollars a sample and achieving Fscores of 0.998.
aws bioinformatics bioinformatics-pipeline budgeting cwl ec2 ephemeral genomic-data-analysis giab human-genome informatics ngs parallel-cluster scalable scaling slurm snakemake snv-call wgs
Last synced: 19 Jun 2025
https://github.com/otiai10/cwl.go
CWL (and input file) parser for Golang, used by github.com/otiai10/yacle
bioinformatics common-workflow-language cwl golang
Last synced: 15 Apr 2025
https://github.com/ohsu-comp-bio/cwl-tes
cwl-tes submits your tasks to a TES server. Task submission is parallelized when possible.
Last synced: 24 Jan 2026
https://github.com/otiai10/yacle
Yet Another CWL Engine by Golang
bioinformatics common-workflow-language cwl
Last synced: 15 Apr 2025
https://github.com/common-workflow-language/cwltest
Framework for testing CWL tools and workflows
Last synced: 19 Aug 2025
https://github.com/common-workflow-language/cwlprov
Profile for provenance research object of a CWL workflow run
bagit cwl cwlprov linked-data prov provenance rdf research-object workflow
Last synced: 20 Jan 2026
https://github.com/dockstore/dockstore-ui2
Website user interface for Dockstore in Angular2
angular cwl dockstore hacktoberfest nextflow wdl
Last synced: 20 Jan 2026
https://github.com/common-workflow-lab/ipython2cwl
IPython2CWL is a tool for converting IPython Jupyter Notebooks to CWL Command Line Tools by simply providing typing annotation.
common-workflow-language cwl docker jupyter jupyter-notebook
Last synced: 02 Feb 2026
https://github.com/nfdi4plants/arctrl
Polyglot (.NET/JS/Python) library for management of Annotated Research Contexts (ARCs) using an in-memory representation and runtime-agnostic contract systems.
arc cwl fable-libraries fair-data fsharp isa rdm ro-crate
Last synced: 07 Apr 2025
https://github.com/aCLImatise/CliHelpParser
Reads the output from CLI help commands, and generates machine readable schemas (CWL etc)
bioinformatics cli cwl parser pipeline wdl workflow
Last synced: 10 Mar 2025
https://github.com/kids-first/kf-somatic-workflow
:microscope: Somatic workflow for Kids-First
bioinformatics cwl drc-harmonization
Last synced: 01 Mar 2026
https://github.com/common-workflow-language/cwljava
Java SDK for the Common Workflow Language standards
Last synced: 19 Aug 2025
https://github.com/kids-first/kf-rnaseq-workflow
:microscope: RNA-Seq workflow for Kids-First DRC
bioinformatics cwl drc-harmonization
Last synced: 01 Mar 2026
https://github.com/maayanlab/playbook-workflow-builder
A repository for the Playbook Workflow Builder project.
bioinformatics biology cwl data-science gene-expression gene-ontology gene-sets proteomics rna-seq-analysis systems-biology workflow
Last synced: 11 Jul 2025
https://github.com/carpentries-incubator/cwl-novice-tutorial
Introduction to Workflows with Common Workflow Language
carpentries-incubator cwl english lesson pre-alpha workflow-management
Last synced: 12 Feb 2026
https://github.com/kids-first/kf-alignment-workflow
:microscope: Alignment workflow for Kids-First DRC
bioinformatics cwl drc-harmonization
Last synced: 01 Mar 2026
https://github.com/rabix/cwl-format
A very opinionated code formatter for CWL
code-formatter common-workflow-language cwl
Last synced: 21 Oct 2025
https://github.com/tom-tan/ep3
A workflow engine for CWL that aims to have a pluggable architecture
common-workflow-language commonwl cwl workflow workflow-engine
Last synced: 14 Apr 2025
https://github.com/tom-tan/cwl-template-for-vscode
A template to write CWL documents with VSCode with remote container extension
common-workflow-language commonwl cwl template vscode
Last synced: 13 Apr 2025
https://github.com/common-workflow-language/cwl-v1.1
Current stable CWL v1.1 specification
Last synced: 30 Jan 2026
https://github.com/wtsi-hgi/gatk-cwl-generator
Generates CWL files from the GATK documentation
Last synced: 28 Oct 2025
https://github.com/truwl/capanno
cwl/wdl/sm/nf files, tool and workflow metadata, and input specifications.
Last synced: 10 Mar 2025
https://github.com/buchanae/cwl
common workflow language library and runtime
Last synced: 22 Mar 2025
https://github.com/tom-tan/cwl-inspector
This tool provides a handy way to inspect properties of tools or workflows written in Common Workflow Language
Last synced: 14 Apr 2025
https://github.com/workflowhub-eu/galaxy2cwl
Standalone version tool to get cwl descriptions (initially an abstract cwl interface) of galaxy workflows and Galaxy workflows executions.
biohackcovid20 cwl galaxy galaxy-workflows ro-crate workflow workflowhub
Last synced: 19 Feb 2026
https://github.com/kids-first/kf-jointgenotyping-workflow
:microscope: Joint genotyping workflow for Kids-First DRC
bioinformatics cwl drc-harmonization
Last synced: 01 Mar 2026
https://github.com/common-workflow-language/cwl-upgrader
Upgrade CWL syntax to a newer version
Last synced: 19 Aug 2025
https://github.com/common-workflow-language/cwlprov-py
cwlprov: Command line tool and Python API to explore Research Objects containing provenance of Common Workflow Language executions
bagit cwl prov provenance python research-object
Last synced: 29 Jan 2026
https://github.com/NAL-i5K/Organism_Onboarding
A workflow to make organism onboarding pipeline easy to handle as an I/O pipeline
Last synced: 10 Mar 2025
https://github.com/onnovalkering/cwl-rs
The Common Workflow Language (CWL) object model for Rust.
Last synced: 03 Jan 2026
https://github.com/xenon-middleware/xenonflow
Run CWL workflows using Xenon through a REST api
Last synced: 10 Mar 2025
https://github.com/giannisdoukas/cwljnikernel
Jupyter Notebook Kernel for Common Workflow Language
common-workflow-language cwl jupyter-notebook workflows
Last synced: 07 Apr 2025
https://github.com/tom-tan/zatsu-cwl-generator
Simple CWL document generator from given execution commands
common-workflow-language commonwl cwl dlang
Last synced: 12 Feb 2026
https://github.com/common-workflow-language/governance
Holds public material generated by and for the CWL board.
Last synced: 13 Feb 2026
https://github.com/ICGC-TCGA-PanCancer/pcawg-snv-indel-annotation
This workflow performs annotation on SNV and INDEL VCFs.
cwl cwl-workflow indel-annotation pcawg snv-annotation
Last synced: 10 Mar 2025
https://github.com/stevekm/minio-workflow-demo
Demo for using MinIO object store with Nextflow and CWL workflows
cwl minio nextflow object-store
Last synced: 04 Mar 2026
https://gitlab.com/m-unlock/cwl
Common Workflow Language - computational workflows
Last synced: 10 Mar 2025
https://github.com/tom-tan/drill-hawk
A visualizer of workflow execution records for CWL
common-workflow-language commonwl cwl visualizer
Last synced: 25 Feb 2026
https://github.com/tom-tan/cwl-conformance-test-summarizer
Summarize the result of conformance test using cwltest
common-workflow-language conformance-tests cwl
Last synced: 27 Mar 2025
https://github.com/giannisdoukas/ipython2cwl-demo
IPython2CWL Demo
common-workflow-language cwl jupyter-notebook
Last synced: 30 Jan 2026
https://github.com/dockstore/dockstore-documentation
The documentation for Dockstore.org
cwl dockstore hacktoberfest nextflow tool wdl workflow
Last synced: 20 Jan 2026
https://github.com/fairagro/m4.4_sciwin_client_examples
Example Projects for SciWIn Client
Last synced: 19 Jan 2026
https://github.com/common-workflow-lab/cwl-d-auto
Autogenerated classes for reading and writing CWL objects using the D language
Last synced: 02 Feb 2026
https://github.com/terradue/calrissian-session
From zero to CWL on K8s with Calrissian
cwl helm-chart kubernetes visual-studio-code
Last synced: 01 Jan 2026
https://github.com/nci-gdc/gdc-somatic-variant-calling-workflow
CWL for GDC somatic variant calling workflow
Last synced: 08 Feb 2026
https://github.com/seanpm2001/Learn-CommonWorkflowLanguage
A repository for showcasing my knowledge of the Common Workflow Language programming language, and continuing to learn the language
article commonworkflowlanguage cwl cwl-lang cwl-language gpl3 gplv3 knowledge learn learn-cwl learn-cwl-lang learn-cwl-language md seanpm2001 seanpm2001-education seanpm2001-learn txt
Last synced: 10 Mar 2025
https://github.com/wtsi-hgi/cwl-graph-generate
Generates https://view.commonwl.org/ like workflows images, showing a complete workflow.
Last synced: 15 Apr 2025
https://github.com/anton-khodak/wdl2cwl
Convert Workflow Definiton Language (WDL) to CWL
Last synced: 10 Mar 2025
https://github.com/anton-khodak/cwl-expression-library
A collection of handy Javascript functions which can be imported in a CWL expression and used for manipulating CWL File objects
Last synced: 07 Apr 2025
https://github.com/Template-Latex/cwl-docs
Archivos autocompletado .cwl para Template-Latex
cwl latex template template-latex
Last synced: 10 Mar 2025
https://github.com/terradue/pycalrissian
Python client for Calrissian - CWL on kubernetes
common-workflow-language cwl kubernetes python
Last synced: 15 Mar 2025
https://github.com/cwl-for-eo/guide
Guide with best practices and examples to adopt CWL in Earth Observation workflows
cwl earth-observation earth-science gdal orfeotoolbox otb snap
Last synced: 10 Mar 2025
https://github.com/common-workflow-lab/run-tests
Action for running tests for CWL workflows
common-workflow-language commonwl cwl testing
Last synced: 02 Feb 2026
https://github.com/nci-gdc/gdc-mirnaseq-cwl
CWL workflows and tools for the miRNA-Seq workflow
Last synced: 25 Jan 2026
https://github.com/r78v10a07/RNASeqWF
This code shows the validation of Differential Gene Expression Analysis from RNASeq data using as quantificator tools TPMCalculator
Last synced: 10 Mar 2025
https://github.com/NLeSC/cwl-tutorial
Simple CWL tutorial based on the gentle introduction to CWL
Last synced: 10 Mar 2025
https://github.com/nanxstats/sbpack-r
An R package to pack and upload CWL apps to Seven Bridges powered platforms
bioinformatics common-workflow-language cwl reticulate
Last synced: 25 Dec 2025
https://github.com/Stefan-Horst/CoCLeagueEvaluator
Creates a player ranking based on Clash of Clans CWL stats taken from Sidekick II Discord Bot for a fair distribution of the bonuses.
clan-war-league clash-of-clans clashofclans coc cwl java player-ranking
Last synced: 10 Mar 2025
https://github.com/suzuki-shm/fastANI-in-cwl
Wrapper tool of fastANI by CWL and Docker
bioinformatics common-workflow-language cwl genome
Last synced: 10 Mar 2025
