cwl

There are 13 repositories under cwl topic.

common-workflow-language
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
Language:Common Workflow Language 1448
DataBiosphere / toil
A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.
cwl python mesos slurm gridengine workflow pipeline aws common-workflow-language kubernetes wdl workflow-description-language
Language:Python 886
arvados / arvados
An open source platform for managing and analyzing biomedical big data
arvados aws azure bigdata bioinformatics cloud cluster cwl docker gcp genomics go python ruby workflow workflow-engine
Language:Go 369
cwltool
common-workflow-language / cwltool
Common Workflow Language reference implementation
common-workflow-language cwl workflows containers science commonwl sciworkflows
Language:Python 326
rabix / composer
Visual and code editor for Common Workflow Language
cwl common-workflow-language ide editor
Language:TypeScript 300
Barski-lab / cwl-airflow
Python package to extend Airflow functionality with CWL1.1 support
cwl-airflow workflow cwl common-workflow-language containers dag cwl-descriptor commonwl
Language:Python 183
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
cancer-imaging-research radiomics radiomics-features machine-learning cpp cpp11 u24 itcr nci nci-itcr nih medical-image-processing cancer cbica image-analysis analytics cwl cwltool medical-image-computing medical-imaging
Language:C++ 174
reanahub / reana
REANA: Reusable research data analysis platform
research-data reproducible-research reproducible-workflows kubernetes containers cwl reusable-science
Language:Python 124
dockstore / dockstore
Our VM/Docker sharing infrastructure and management component
dockstore docker cwl wdl containers bioinformatics nextflow workflow
Language:Java 117
EBI-Metagenomics / emg-viral-pipeline
VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
nextflow viruses cwl workflow pipeline
Language:Python 112
ga4gh / workflow-execution-service-schemas
The WES API is a standard way to run and manage portable workflows.
workflow cwl wdl ga4gh
82
common-workflow-library / bio-cwl-tools
CWL CommandLineTool descriptions for biology/life-sciences related applications
cwl
Language:Common Workflow Language 75
rabix / cwl-svg
A library for generating an interactive SVG visualization of CWL workflows
cwl svg workflow visualization bioinformatics
Language:TypeScript 75
rabix / bunny
[Legacy] Executor for CWL workflows. Executes sbg:draft-2 and CWL 1.0
cwl workflow docker executor java common-workflow-language commonwl
Language:Common Workflow Language 74
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.
pipelines aws-step-function aws docker aws-lambda bioinformatics cwl wdl cwl-workflow wdl-workflow snakemake snakemake-workflow conda
Language:Python 70
benten
rabix / benten
A language server for Common Workflow Language
common-workflow-language cwl workflow editor language-server cwl-documents ide
Language:Python 67
rabix / cwl-ts
Typescript data model for Common Workflow Language
common-workflow-language workflow cwl typescript
Language:TypeScript 49
ResearchObject / ro-crate-py
Python library for RO-Crate
metadata ro-crate researchobject galaxy cwl biohackcovid20 biohackeu20
Language:Jupyter Notebook 44
cwlviewer
common-workflow-language / cwlviewer
A web application to view and share Common Workflow Language workflows
cwl common-workflow-language workflow workflows java
Language:Java 42
Duke-GCB / calrissian
CWL on Kubernetes
cwl cwl-workflow cwl-workflows kubernetes
Language:Python 42
user_guide
common-workflow-language / user_guide
The CWL v1.0 - v1.2 user guide
cwl common-workflow-language workflow workflows
Language:Common Workflow Language 41
NLeSC / scriptcwl
Create cwl workflows by writing a simple Python script
cwl workflow python
Language:Python 40
PMCC-BioinformaticsCore / janis
[Alpha] Janis: an open source tool to machine generate type-safe CWL and WDL workflows
workflow common-workflow-language workflow-description-language cwl wdl python
Language:Python 40
yuch7 / cwlexec
A new open source tool to run CWL workflows on LSF
workflow lsf cwl java
Language:Java 36
nlppln / nlppln
NLP pipeline software using common workflow language
nlp cwl workflow pipeline text-mining
Language:Python 34
cwl-utils
common-workflow-language / cwl-utils
Python utilities for CWL
cwl common-workflow-language commonwl
Language:Python 33
yyoshiaki / VIRTUS
A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.
virus-detection rnaseq cwl
Language:Common Workflow Language 33
stjudecloud / workflows
Bioinformatics workflows developed for and used on the St. Jude Cloud project.
bioinformatics-workflows workflows cromwell wdl bioinformatics computational-biology workflow workflow-engine next-generation-sequencing genomics stjudecloud wdl-workflow cwl cwl-workflow
Language:WDL 32
dnanexus / dxCompiler
WDL and CWL compiler for the DNAnexus platform
compiler cwl dnanexus wdl
Language:Scala 31
ga4gh / tool-registry-service-schemas
APIs for discovering genomics tools, their metadata and their containers
ga4gh api tool workflow cwl wdl
Language:Shell 30
otiai10 / hotsub
Command line tool to run batch jobs concurrently with ETL framework on AWS or other cloud computing resources
workflow workflow-engine etl-framework bioinformatics cwl cwl-workflow wdl wdl-workflow batch-job aws gcp docker docker-machine
Language:Go 30
common-workflow-lab / wdl2cwl
[Experimental] Workflow Definition Language (WDL) to CWL
commonwl cwl wdl wdl-workflow
Language:Python 28
common-workflow-lab / wdl-cwl-translator
A translator from WDL to CWL v1.2
commonwl cwl wdl
Language:Common Workflow Language 26
crim-ca / weaver
Weaver: Workflow Execution Management Service (EMS); Application, Deployment and Execution Service (ADES); OGC API - Processes; WPS; CWL Application Package
ogc wps cwl workflow remote-execution ems ades common-workflow-language web-application web-processing-service
Language:Python 24
otiai10 / cwl.go
CWL (and input file) parser for Golang, used by github.com/otiai10/yacle
cwl common-workflow-language golang bioinformatics
Language:Go 22
EBI-Metagenomics / pipeline-v5
This repository contains all CWL descriptions of the MGnify pipeline version 5.0.
common-workflow-language cwl workflow cwl-descriptions cwl-workflow mgnify metagenomic-pipeline metagenomic-analysis metagenomic-classification metagenomic-data metagenomics amplicon-pipeline wgs-analysis
Language:HTML 21

cwl

common-workflow-language / common-workflow-language

DataBiosphere / toil

arvados / arvados

common-workflow-language / cwltool

rabix / composer

Barski-lab / cwl-airflow

CBICA / CaPTk

reanahub / reana

dockstore / dockstore

EBI-Metagenomics / emg-viral-pipeline

ga4gh / workflow-execution-service-schemas

common-workflow-library / bio-cwl-tools

rabix / cwl-svg

rabix / bunny

4dn-dcic / tibanna

rabix / benten

rabix / cwl-ts

ResearchObject / ro-crate-py

common-workflow-language / cwlviewer

Duke-GCB / calrissian

common-workflow-language / user_guide

NLeSC / scriptcwl

PMCC-BioinformaticsCore / janis

yuch7 / cwlexec

nlppln / nlppln

common-workflow-language / cwl-utils

yyoshiaki / VIRTUS

stjudecloud / workflows

dnanexus / dxCompiler

ga4gh / tool-registry-service-schemas

otiai10 / hotsub

common-workflow-lab / wdl2cwl

common-workflow-lab / wdl-cwl-translator

crim-ca / weaver

otiai10 / cwl.go

EBI-Metagenomics / pipeline-v5