cwl | Topic | Ecosyste.ms: Repos

Topic: "cwl"

common-workflow-language/common-workflow-language

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

Language: Common Workflow Language - Size: 3.63 MB - Last synced at: 7 days ago - Pushed at: 5 months ago - Stars: 1,464 - Forks: 195

DataBiosphere/toil

A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.

Language: Python - Size: 34.2 MB - Last synced at: 6 days ago - Pushed at: 7 days ago - Stars: 909 - Forks: 241

arvados/arvados

An open source platform for managing and analyzing biomedical big data

Language: Go - Size: 75.4 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 403 - Forks: 121

common-workflow-language/cwltool

Common Workflow Language reference implementation

Language: Python - Size: 11.3 MB - Last synced at: 1 day ago - Pushed at: 8 days ago - Stars: 348 - Forks: 231

rabix/composer

Visual and code editor for Common Workflow Language

Language: TypeScript - Size: 13.3 MB - Last synced at: 10 days ago - Pushed at: over 2 years ago - Stars: 303 - Forks: 72

Barski-lab/cwl-airflow

Python package to extend Airflow functionality with CWL1.1 support

Language: Python - Size: 2.77 MB - Last synced at: 16 days ago - Pushed at: over 1 year ago - Stars: 187 - Forks: 32

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

Language: C++ - Size: 239 MB - Last synced at: 6 months ago - Pushed at: over 1 year ago - Stars: 180 - Forks: 64

EBI-Metagenomics/emg-viral-pipeline

VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies

Language: Python - Size: 28.9 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 132 - Forks: 18

reanahub/reana

REANA: Reusable research data analysis platform

Language: Python - Size: 2.89 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 132 - Forks: 55

dockstore/dockstore

An app store for scientific workflows, tools, notebooks, and services

Language: Java - Size: 40.6 MB - Last synced at: about 13 hours ago - Pushed at: about 14 hours ago - Stars: 125 - Forks: 29

ga4gh/workflow-execution-service-schemas

The WES API is a standard way to run and manage portable workflows.

Size: 4.42 MB - Last synced at: about 2 months ago - Pushed at: 7 months ago - Stars: 83 - Forks: 39

common-workflow-library/bio-cwl-tools

CWL CommandLineTool descriptions for biology/life-sciences related applications

Language: Common Workflow Language - Size: 724 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 78 - Forks: 38

rabix/cwl-svg

A library for generating an interactive SVG visualization of CWL workflows

Language: TypeScript - Size: 10.9 MB - Last synced at: 19 days ago - Pushed at: 9 months ago - Stars: 77 - Forks: 18

rabix/bunny

[Legacy] Executor for CWL workflows. Executes sbg:draft-2 and CWL 1.0

Language: Common Workflow Language - Size: 5.75 MB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 74 - Forks: 28

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.

Language: Python - Size: 134 MB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 69 - Forks: 27

rabix/benten

A language server for Common Workflow Language

Language: Python - Size: 5.06 MB - Last synced at: 16 days ago - Pushed at: over 1 year ago - Stars: 65 - Forks: 9

ResearchObject/ro-crate-py

Python library for RO-Crate

Language: Jupyter Notebook - Size: 1.03 MB - Last synced at: 23 days ago - Pushed at: about 2 months ago - Stars: 62 - Forks: 31

rabix/cwl-ts

Typescript data model for Common Workflow Language

Language: TypeScript - Size: 2.49 MB - Last synced at: 10 days ago - Pushed at: about 2 years ago - Stars: 49 - Forks: 19

Duke-GCB/calrissian

CWL on Kubernetes

Language: Python - Size: 1010 KB - Last synced at: 26 days ago - Pushed at: 5 months ago - Stars: 47 - Forks: 17

common-workflow-language/cwlviewer

A web application to view and share Common Workflow Language workflows

Language: Java - Size: 10.1 MB - Last synced at: about 3 hours ago - Pushed at: about 4 hours ago - Stars: 46 - Forks: 28

PMCC-BioinformaticsCore/janis

[Alpha] Janis: an open source tool to machine generate type-safe CWL and WDL workflows

Language: Python - Size: 16 MB - Last synced at: 17 days ago - Pushed at: over 1 year ago - Stars: 43 - Forks: 13

common-workflow-language/user_guide

The CWL v1.0 - v1.2 user guide

Language: Common Workflow Language - Size: 18.3 MB - Last synced at: 22 days ago - Pushed at: 7 months ago - Stars: 42 - Forks: 68

NLeSC/scriptcwl

Create cwl workflows by writing a simple Python script

Language: Python - Size: 352 KB - Last synced at: 25 days ago - Pushed at: about 5 years ago - Stars: 40 - Forks: 9

common-workflow-language/cwl-utils

Python utilities for CWL

Language: Python - Size: 1.73 MB - Last synced at: 1 day ago - Pushed at: about 2 months ago - Stars: 39 - Forks: 18

stjudecloud/workflows

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

Language: WDL - Size: 74.7 MB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 36 - Forks: 12

yuch7/cwlexec

A new open source tool to run CWL workflows on LSF

Language: Java - Size: 24 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 36 - Forks: 8

yyoshiaki/VIRTUS

A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.

Language: Common Workflow Language - Size: 9.62 MB - Last synced at: about 2 months ago - Pushed at: about 3 years ago - Stars: 34 - Forks: 9

dnanexus/dxCompiler

WDL and CWL compiler for the DNAnexus platform

Language: Scala - Size: 10.9 MB - Last synced at: 29 days ago - Pushed at: 29 days ago - Stars: 33 - Forks: 17

nlppln/nlppln

NLP pipeline software using common workflow language

Language: Python - Size: 266 KB - Last synced at: 23 days ago - Pushed at: about 6 years ago - Stars: 33 - Forks: 3

ga4gh/tool-registry-service-schemas

APIs for discovering genomics tools, their metadata and their containers

Language: Shell - Size: 9.57 MB - Last synced at: about 2 months ago - Pushed at: 6 months ago - Stars: 31 - Forks: 18

otiai10/hotsub

Command line tool to run batch jobs concurrently with ETL framework on AWS or other cloud computing resources

Language: Go - Size: 283 KB - Last synced at: 3 days ago - Pushed at: over 6 years ago - Stars: 30 - Forks: 5

crim-ca/weaver

Weaver: Workflow Execution Management Service (EMS); Application, Deployment and Execution Service (ADES); OGC API - Processes; WPS; CWL Application Package

Language: Python - Size: 95.9 MB - Last synced at: 5 days ago - Pushed at: 6 days ago - Stars: 28 - Forks: 6

common-workflow-lab/wdl2cwl 📦

[Experimental] Workflow Definition Language (WDL) to CWL

Language: Python - Size: 179 KB - Last synced at: 12 days ago - Pushed at: over 3 years ago - Stars: 28 - Forks: 4

common-workflow-lab/wdl-cwl-translator

A translator from WDL to CWL v1.2

Language: Common Workflow Language - Size: 14.9 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 26 - Forks: 8

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.

Language: Python - Size: 339 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 23 - Forks: 2

NCI-GDC/gdc-dnaseq-cwl

CWL for GDC DNASeq workflows

Language: Common Workflow Language - Size: 194 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 22 - Forks: 14

otiai10/cwl.go

CWL (and input file) parser for Golang, used by github.com/otiai10/yacle

Language: Go - Size: 582 KB - Last synced at: 21 days ago - Pushed at: about 6 years ago - Stars: 22 - Forks: 7

EBI-Metagenomics/pipeline-v5

This repository contains all CWL descriptions of the MGnify pipeline version 5.0.

Language: HTML - Size: 376 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 21 - Forks: 20

sbg/sevenbridges-cwl

Seven Bridges Python library for programatic generation of CWL workflows.

Language: Python - Size: 1.3 MB - Last synced at: 19 days ago - Pushed at: over 2 years ago - Stars: 20 - Forks: 3

Duke-GCB/GGR-cwl

CWL tools and workflows for GGR

Language: Common Workflow Language - Size: 723 KB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 20 - Forks: 17

TheJacksonLaboratory/CloudNeo

CWL implementation of CloudNeo: A cloud pipeline for identifying patient-specific tumor neoantigens

Language: Common Workflow Language - Size: 15.1 MB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 19 - Forks: 11

ohsu-comp-bio/cwl-tes

cwl-tes submits your tasks to a TES server. Task submission is parallelized when possible.

Language: Python - Size: 253 KB - Last synced at: 11 days ago - Pushed at: about 2 years ago - Stars: 18 - Forks: 28

otiai10/yacle

Yet Another CWL Engine by Golang

Language: Go - Size: 87.9 KB - Last synced at: 21 days ago - Pushed at: about 6 years ago - Stars: 18 - Forks: 3

nfdi4plants/ARCtrl

Polyglot (.NET/JS/Python) library for management of Annotated Research Contexts (ARCs) using an in-memory representation and runtime-agnostic contract systems.

Language: F# - Size: 9.99 MB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 17 - Forks: 8

common-workflow-language/cwltest

Framework for testing CWL tools and workflows

Language: Python - Size: 480 KB - Last synced at: 21 days ago - Pushed at: about 2 months ago - Stars: 17 - Forks: 18

common-workflow-language/cwlprov

Profile for provenance research object of a CWL workflow run

Size: 140 KB - Last synced at: about 1 month ago - Pushed at: over 2 years ago - Stars: 17 - Forks: 3

datirium/workflows

CWL based Bioinformatics Workflows

Language: Common Workflow Language - Size: 3.32 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 16 - Forks: 16

dockstore/dockstore-ui2

Website user interface for Dockstore in Angular2

Language: TypeScript - Size: 42.6 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 16 - Forks: 16

antonjan/Raspberry_Telemetry

This project will have the files for a Cube Sat Telemetry system Using Raspberry Pi Transmitter Board

Language: Shell - Size: 36.6 MB - Last synced at: about 1 year ago - Pushed at: about 7 years ago - Stars: 16 - Forks: 4

common-workflow-lab/ipython2cwl

IPython2CWL is a tool for converting IPython Jupyter Notebooks to CWL Command Line Tools by simply providing typing annotation.

Language: Python - Size: 329 KB - Last synced at: 9 months ago - Pushed at: over 2 years ago - Stars: 15 - Forks: 5

aCLImatise/CliHelpParser

Reads the output from CLI help commands, and generates machine readable schemas (CWL etc)

Language: Python - Size: 1.16 MB - Last synced at: 17 days ago - Pushed at: about 4 years ago - Stars: 14 - Forks: 6

Consonance/consonance

Core consonance utilities for scheduling, reporting on, and provisioning VMs for workflows

Language: Java - Size: 3.81 MB - Last synced at: about 2 months ago - Pushed at: almost 7 years ago - Stars: 14 - Forks: 5

kids-first/kf-somatic-workflow

:microscope: Somatic workflow for Kids-First

Language: Common Workflow Language - Size: 8.44 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 13 - Forks: 2

common-workflow-language/cwljava

Java SDK for the Common Workflow Language standards

Language: Java - Size: 10.8 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 13 - Forks: 8

rworkflow/Rcwl

Write CWL in R

Language: R - Size: 2.49 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 13 - Forks: 4

workflowhub-eu/about

Website about the project WorkflowHub

Language: HTML - Size: 5.76 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 12 - Forks: 18

ebi-jdispatcher/webservice-cwl

Programmatic access to various data resources and analysis EBI tools via CWL

Language: Common Workflow Language - Size: 958 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 12 - Forks: 3

kids-first/kf-rnaseq-workflow

:microscope: RNA-Seq workflow for Kids-First DRC

Language: Common Workflow Language - Size: 1.46 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 11 - Forks: 8

kids-first/kf-alignment-workflow

:microscope: Alignment workflow for Kids-First DRC

Language: Common Workflow Language - Size: 2.81 MB - Last synced at: 10 days ago - Pushed at: 11 days ago - Stars: 11 - Forks: 6

MaayanLab/Playbook-Workflow-Builder

A repository for the Playbook Workflow Builder project.

Language: TypeScript - Size: 20.8 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 11 - Forks: 18

carpentries-incubator/cwl-novice-tutorial

Introduction to Workflows with Common Workflow Language

Language: HTML - Size: 5.24 MB - Last synced at: 3 months ago - Pushed at: about 1 year ago - Stars: 11 - Forks: 20

arunisaac/ravanan

High-reproducibility CWL runner powered by Guix

Language: Scheme - Size: 1.1 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 10 - Forks: 0

common-workflow-language/cwl-website

www.commonwl.org

Language: JavaScript - Size: 13.5 MB - Last synced at: 29 days ago - Pushed at: about 2 months ago - Stars: 10 - Forks: 20

tom-tan/ep3

A workflow engine for CWL that aims to have a pluggable architecture

Language: Ruby - Size: 386 KB - Last synced at: 15 days ago - Pushed at: about 3 years ago - Stars: 10 - Forks: 3

NCBI-Hackathons/Virus_Detection_SRA

Language: Perl - Size: 52.7 KB - Last synced at: about 2 months ago - Pushed at: over 7 years ago - Stars: 10 - Forks: 9

4dn-dcic/pipelines-cwl

Pipelines developed and used by 4DN-DCIC in Common Workflow Language

Language: Common Workflow Language - Size: 237 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 9 - Forks: 4

rabix/cwl-format

A very opinionated code formatter for CWL

Language: Common Workflow Language - Size: 202 KB - Last synced at: 16 days ago - Pushed at: over 1 year ago - Stars: 9 - Forks: 4

truwl/capanno

cwl/wdl/sm/nf files, tool and workflow metadata, and input specifications.

Language: wdl - Size: 19.5 MB - Last synced at: 10 days ago - Pushed at: about 3 years ago - Stars: 9 - Forks: 4

ga4gh/cloud-interop-testing

Interoperable execution of workflows using GA4GH APIs

Language: Python - Size: 1.29 MB - Last synced at: about 2 months ago - Pushed at: almost 4 years ago - Stars: 9 - Forks: 8

ResearchObject/workflow-run-crate

Workflow Run RO-Crate profile

Language: Python - Size: 56.7 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 8 - Forks: 10

tom-tan/cwl-template-for-vscode

A template to write CWL documents with VSCode with remote container extension

Language: Dockerfile - Size: 56.6 KB - Last synced at: 23 days ago - Pushed at: 8 months ago - Stars: 8 - Forks: 3

NCBI-Hackathons/Epigenomics_CWL

SCREW: A Reproducible Workflow for Single-Cell Epigenomics

Language: R - Size: 39.9 MB - Last synced at: about 1 year ago - Pushed at: over 7 years ago - Stars: 8 - Forks: 15

common-workflow-language/cwl-v1.1

Current stable CWL v1.1 specification

Language: Common Workflow Language - Size: 1.46 MB - Last synced at: about 1 month ago - Pushed at: 5 months ago - Stars: 7 - Forks: 11

tom-tan/cwl-inspector

This tool provides a handy way to inspect properties of tools or workflows written in Common Workflow Language

Language: Ruby - Size: 364 KB - Last synced at: 15 days ago - Pushed at: over 3 years ago - Stars: 7 - Forks: 2

buchanae/cwl

common workflow language library and runtime

Language: Go - Size: 274 KB - Last synced at: 28 days ago - Pushed at: over 6 years ago - Stars: 7 - Forks: 3

wtsi-hgi/gatk-cwl-generator

Generates CWL files from the GATK documentation

Language: Python - Size: 42.5 MB - Last synced at: 21 days ago - Pushed at: almost 7 years ago - Stars: 7 - Forks: 1

kids-first/kf-jointgenotyping-workflow

:microscope: Joint genotyping workflow for Kids-First DRC

Language: Common Workflow Language - Size: 2.15 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 6 - Forks: 1

EBI-Metagenomics/workflow-is-cwl

This repository contains CWL descriptions of the various tools which will allow you to build workflows for the annotation of transcripts

Language: HTML - Size: 30.6 MB - Last synced at: about 1 year ago - Pushed at: almost 5 years ago - Stars: 6 - Forks: 7

fairagro/m4.4_sciwin_client

🦀 SciWIn Client: Reproducible computational Workflows made easy!

Language: Rust - Size: 1.86 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 5 - Forks: 1

msk-access/cwl-commandlinetools Fork of mskcc/cwl-commandlinetools

Central location for CWL CommandLineTools

Language: Common Workflow Language - Size: 1.13 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 5 - Forks: 0

common-workflow-language/cwl-upgrader

Upgrade CWL syntax to a newer version

Language: Python - Size: 225 KB - Last synced at: 9 days ago - Pushed at: 3 months ago - Stars: 5 - Forks: 3

workflowhub-eu/galaxy2cwl

Standalone version tool to get cwl descriptions (initially an abstract cwl interface) of galaxy workflows and Galaxy workflows executions.

Language: Python - Size: 96.7 KB - Last synced at: 22 days ago - Pushed at: about 3 years ago - Stars: 5 - Forks: 5

onnovalkering/cwl-rs

The Common Workflow Language (CWL) object model for Rust.

Language: Common Workflow Language - Size: 53.7 KB - Last synced at: 24 days ago - Pushed at: over 3 years ago - Stars: 5 - Forks: 1

eliza-m/CrossSpeciesWorkflow

CWL workflow that facilitate performing a series of structural and phenotype related third party prediction methods starting from either a protein FASTA file or a list of Uniprot IDs. Integrated prediction methods refer to secondary structure, solvent accessibility, disordered regions, PTS modifications (phosphorylation, glycosylation, lipid modification, sumoylation, etc).

Language: Python - Size: 6.13 MB - Last synced at: about 2 months ago - Pushed at: over 4 years ago - Stars: 5 - Forks: 3