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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: 2024-11-08 00:06:48 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: 15 Oct 2024
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: 06 Nov 2024
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: 06 Aug 2024
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: 03 Aug 2024
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 pipelines snakemake snakemake-workflow wdl wdl-workflow
Last synced: 08 Nov 2024
https://github.com/Duke-GCB/calrissian
CWL on Kubernetes
cwl cwl-workflow cwl-workflows kubernetes
Last synced: 23 Oct 2024
https://github.com/NLeSC/scriptcwl
Create cwl workflows by writing a simple Python script
Last synced: 23 Oct 2024
https://github.com/nlppln/nlppln
NLP pipeline software using common workflow language
cwl nlp pipeline text-mining workflow
Last synced: 23 Oct 2024
https://github.com/yyoshiaki/VIRTUS
A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.
Last synced: 23 Oct 2024
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: 08 Nov 2024
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: 08 Nov 2024
https://github.com/otiai10/yacle
Yet Another CWL Engine by Golang
bioinformatics common-workflow-language cwl
Last synced: 16 Oct 2024
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: 23 Oct 2024
https://github.com/tom-tan/ep3
A workflow engine for CWL which aims to have a pluggable architecture
common-workflow-language commonwl cwl workflow workflow-engine
Last synced: 15 Oct 2024
https://github.com/kids-first/kf-rnaseq-workflow
:microscope: RNA-Seq workflow for Kids-First DRC
bioinformatics cwl drc-harmonization
Last synced: 23 Oct 2024
https://github.com/truwl/capanno
cwl/wdl/sm/nf files, tool and workflow metadata, and input specifications.
Last synced: 23 Oct 2024
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: 15 Oct 2024
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: 15 Oct 2024
https://github.com/xenon-middleware/xenonflow
Run CWL workflows using Xenon through a REST api
Last synced: 23 Oct 2024
https://github.com/giannisdoukas/cwljnikernel
Jupyter Notebook Kernel for Common Workflow Language
common-workflow-language cwl jupyter-notebook workflows
Last synced: 06 Nov 2024
https://gitlab.com/m-unlock/cwl
Common Workflow Language - computational workflows
Last synced: 23 Oct 2024
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: 23 Oct 2024
https://github.com/tom-tan/zatsu-cwl-generator
Simple CWL document generator from given execution commands
common-workflow-language commonwl cwl dlang
Last synced: 15 Oct 2024
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: 23 Oct 2024
https://github.com/onnovalkering/cwl-rs
The Common Workflow Language (CWL) object model for Rust.
Last synced: 23 Oct 2024
https://github.com/NAL-i5K/Organism_Onboarding
A workflow to make organism onboarding pipeline easy to handle as an I/O pipeline
Last synced: 23 Oct 2024
https://github.com/tom-tan/drill-hawk
A visualizer of workflow execution records for CWL
common-workflow-language commonwl cwl visualizer
Last synced: 15 Oct 2024
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: 15 Oct 2024
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: 23 Oct 2024
https://github.com/anton-khodak/wdl2cwl
Convert Workflow Definiton Language (WDL) to CWL
Last synced: 23 Oct 2024
https://github.com/wtsi-hgi/cwl-graph-generate
Generates https://view.commonwl.org/ like workflows images, showing a complete workflow.
Last synced: 23 Oct 2024
https://github.com/giannisdoukas/ipython2cwl-demo
IPython2CWL Demo
common-workflow-language cwl jupyter-notebook
Last synced: 15 Oct 2024
https://github.com/Template-Latex/cwl-docs
Archivos autocompletado .cwl para Template-Latex
cwl latex template template-latex
Last synced: 23 Oct 2024
https://github.com/common-workflow-lab/cwl-d-auto
Autogenerated classes for reading and writing CWL objects using the D language
Last synced: 23 Oct 2024
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: 03 Nov 2024
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: 23 Oct 2024
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: 23 Oct 2024
https://github.com/NLeSC/cwl-tutorial
Simple CWL tutorial based on the gentle introduction to CWL
Last synced: 23 Oct 2024
https://github.com/suzuki-shm/fastANI-in-cwl
Wrapper tool of fastANI by CWL and Docker
bioinformatics common-workflow-language cwl genome
Last synced: 23 Oct 2024
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: 23 Oct 2024
https://github.com/GusEllerm/GIS_IndexGen
Prototype implementation of LivePaper with GIS indices as the subject.
cwl cwl-workflow gis livedata livepaper remote-sensing
Last synced: 23 Oct 2024
https://github.com/Terradue/ogc-eo-application-package-hands-on
OGC EO Application Package Hands-on
cwl cwl-workflow earth-observation eo python sentinel-2
Last synced: 23 Oct 2024
https://github.com/NCI-GDC/gdc-sanger-somatic-cwl
CWL Workflows for the Sanger Somatic Workflow
Last synced: 23 Oct 2024
https://github.com/dockstore/dockstore-training
Working space for creating dockstore training materials
Last synced: 23 Oct 2024
https://github.com/inab/ipc_workflows
iPC Workflows for VRE
cwl ipc ipc-project nextflow singularity vre workflows
Last synced: 10 Nov 2024
https://github.com/tom-tan/conformance
Location to store the results of CWL conformance testing for ep3
common-workflow-language commonwl cwl
Last synced: 15 Oct 2024
https://github.com/fairagro/M4.4_UC6_ARC
UC6 workflow in ARC proof-of-concept
common-workflow-language cwl fairagro
Last synced: 23 Oct 2024
https://github.com/systemPipeR/SPblast
BLAST Workflow Template
analysis-pipeline blast cwl development systempiper systempiper-workflows workflow
Last synced: 23 Oct 2024
https://github.com/COV-IRT/d3b-dev-rnaseq-snv
RNAseq SNV Calling Workflow (beta)
Last synced: 23 Oct 2024
https://github.com/bernddoser/ml-workflow-orchestration
Seminar: Machine Learning Workflow Orchestration
cwl flyte machine-learning workflow
Last synced: 27 Oct 2024
https://github.com/fpsom/intro-to-cwl-docker
Introduction to CWL and Docker
Last synced: 23 Oct 2024
https://github.com/NCI-GDC/samtools-mpileup-cwl
CWL for GDC samtools mpileup
Last synced: 23 Oct 2024
https://github.com/mattdoug604/help-to-cwl
Automatically generate a bare-bones CWL tool for your program of interest.
Last synced: 09 Nov 2024
