Barski-lab/cwl-airflow

Python package to extend Airflow functionality with CWL1.1 support

Language: Python - Size: 2.77 MB - Last synced: about 11 hours ago - Pushed: 7 months ago - Stars: 184 - Forks: 34

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: 96 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 22 - Forks: 5

kids-first/kf-rnaseq-workflow

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

Language: Common Workflow Language - Size: 1.32 MB - Last synced: 1 day ago - Pushed: 3 days ago - Stars: 9 - Forks: 8

common-workflow-language/cwltool

Common Workflow Language reference implementation

Language: Python - Size: 11.2 MB - Last synced: about 23 hours ago - Pushed: 2 days ago - Stars: 321 - Forks: 224

common-workflow-language/user_guide

The CWL v1.0 - v1.2 user guide

Language: Common Workflow Language - Size: 18.3 MB - Last synced: about 24 hours ago - Pushed: 2 days ago - Stars: 39 - Forks: 66

DataBiosphere/toil

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

Language: Python - Size: 33.1 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 874 - Forks: 236

dockstore/dockstore

Our VM/Docker sharing infrastructure and management component

Language: Java - Size: 40.2 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 115 - Forks: 28

common-workflow-language/cwl-upgrader

Upgrade CWL syntax to a newer version

Language: Python - Size: 214 KB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 5 - Forks: 3

common-workflow-language/cwl-website

www.commonwl.org

Language: JavaScript - Size: 13.4 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 11 - Forks: 20

arvados/arvados

An open source platform for managing and analyzing biomedical big data

Language: Go - Size: 72.7 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 364 - Forks: 112

rworkflow/RcwlRecipes

Language: Common Workflow Language - Size: 399 KB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 2 - Forks: 2

datirium/workflows

CWL based Bioinformatics Workflows

Language: Common Workflow Language - Size: 2.86 MB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 14 - Forks: 13

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.

Language: Python - Size: 134 MB - Last synced: 2 days ago - Pushed: 3 months ago - Stars: 69 - Forks: 27

kids-first/kf-somatic-workflow

:microscope: Somatic workflow for Kids-First

Language: Common Workflow Language - Size: 8.31 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 10 - Forks: 2

umccr/cwl-novice-tutorial

CWL Novice Tutorial

Language: HTML - Size: 6.59 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 0 - Forks: 0

stjudecloud/workflows

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

Language: WDL - Size: 9.76 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 30 - Forks: 9

stevekm/cwl-nf

Run Nextflow from within a CWL pipeline

Language: Makefile - Size: 5.86 KB - Last synced: 8 days ago - Pushed: about 4 years ago - Stars: 1 - Forks: 0

ResearchObject/workflow-run-crate

Workflow Run RO-Crate profile

Language: Python - Size: 56.5 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 8 - Forks: 9

ResearchObject/ro-crate-py

Python library for RO-Crate

Language: Jupyter Notebook - Size: 1.09 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 42 - Forks: 21

common-workflow-language/cwlviewer

A web application to view and share Common Workflow Language workflows

Language: Java - Size: 10.1 MB - Last synced: 10 days ago - Pushed: 11 days ago - Stars: 40 - Forks: 27

rworkflow/Rcwl

Write CWL in R

Language: R - Size: 2.49 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 13 - Forks: 4

EBI-Metagenomics/emg-viral-pipeline

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

Language: Python - Size: 28.8 MB - Last synced: 11 days ago - Pushed: 12 days ago - Stars: 107 - Forks: 13

reanahub/reana

REANA: Reusable research data analysis platform

Language: Python - Size: 2.82 MB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 121 - Forks: 50

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: 11 days ago - Pushed: 6 months ago - Stars: 1,442 - Forks: 199

common-workflow-language/cwljava

Java SDK for the Common Workflow Language standards

Language: Java - Size: 10.7 MB - Last synced: 13 days ago - Pushed: 14 days ago - Stars: 12 - Forks: 8

rabix/cwl-ts

Typescript data model for Common Workflow Language

Language: TypeScript - Size: 2.49 MB - Last synced: 15 days ago - Pushed: about 1 year ago - Stars: 49 - Forks: 19

workflowhub-eu/about

Website about the project WorkflowHub

Language: HTML - Size: 5.73 MB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 9 - Forks: 17

common-workflow-language/cwl-utils

Python utilities for CWL

Language: Python - Size: 1.27 MB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 31 - Forks: 17

Duke-GCB/calrissian

CWL on Kubernetes

Language: Python - Size: 1.19 MB - Last synced: 17 days ago - Pushed: 18 days ago - Stars: 40 - Forks: 13

kids-first/kf-jointgenotyping-workflow

:microscope: Joint genotyping workflow for Kids-First DRC

Language: Common Workflow Language - Size: 2.16 MB - Last synced: 17 days ago - Pushed: 18 days ago - Stars: 6 - Forks: 1

NAL-i5K/Organism_Onboarding

A workflow to make organism onboarding pipeline easy to handle as an I/O pipeline

Language: Common Workflow Language - Size: 5.91 MB - Last synced: 18 days ago - Pushed: 19 days ago - Stars: 4 - Forks: 1

seanpm2001/SNU_2D_ProgrammingTools_IDE_CommonWorkflowLanguage

The Common Workflow Language Programming language IDE submodule for SNU Programming Tools (2D Mode)

Language: Common Workflow Language - Size: 499 KB - Last synced: 22 days ago - Pushed: over 1 year ago - Stars: 2 - Forks: 1

seanpm2001/Learn-CommonWorkflowLanguage

A repository for showcasing my knowledge of the Common Workflow Language programming language, and continuing to learn the language

Language: Common Workflow Language - Size: 452 KB - Last synced: 22 days ago - Pushed: over 1 year ago - Stars: 2 - Forks: 1

r78v10a07/RNASeqWF

This code shows the validation of Differential Gene Expression Analysis from RNASeq data using as quantificator tools TPMCalculator

Language: HTML - Size: 57.5 MB - Last synced: 26 days ago - Pushed: over 5 years ago - Stars: 1 - Forks: 0

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: 12 days ago - Pushed: 5 months ago - Stars: 169 - Forks: 63

Terradue/pycalrissian

Python client for Calrissian - CWL on kubernetes

Language: Python - Size: 547 KB - Last synced: about 1 month ago - Pushed: 6 months ago - Stars: 2 - Forks: 1

common-workflow-language/cwltest

Framework for testing CWL tools and workflows

Language: Python - Size: 440 KB - Last synced: about 2 months ago - Pushed: 2 months ago - Stars: 17 - Forks: 17

dockstore/dockstore-ui2

Website user interface for Dockstore in Angular2

Language: TypeScript - Size: 39.8 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 15 - Forks: 16

inab/ipc_workflows

iPC Workflows for VRE

Language: Common Workflow Language - Size: 118 KB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

NCI-GDC/sesame-cwl

GDC Methylation Array Workflow

Language: Common Workflow Language - Size: 104 KB - Last synced: about 1 month ago - Pushed: 3 months ago - Stars: 1 - Forks: 0

NCI-GDC/gdc-somatic-variant-calling-workflow

CWL for GDC somatic variant calling workflow

Language: Common Workflow Language - Size: 154 KB - Last synced: about 1 month ago - Pushed: 6 months ago - Stars: 1 - Forks: 2

NCI-GDC/gdc-mirnaseq-cwl

CWL workflows and tools for the miRNA-Seq workflow

Language: Common Workflow Language - Size: 148 KB - Last synced: about 1 month ago - Pushed: 6 months ago - Stars: 0 - Forks: 1

NCI-GDC/htseq-cwl 📦

HTSeq CWL Workflow

Language: Common Workflow Language - Size: 49.8 KB - Last synced: about 1 month ago - Pushed: 10 months ago - Stars: 2 - Forks: 2

NCI-GDC/gdc_tosvc_workflow

GDC Tumor-only Somatic Variant Calling Workflow

Language: Common Workflow Language - Size: 277 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

NCI-GDC/gdc-sanger-somatic-cwl

CWL Workflows for the Sanger Somatic Workflow

Language: Common Workflow Language - Size: 75.2 KB - Last synced: about 1 month ago - Pushed: 6 months ago - Stars: 0 - Forks: 2

common-workflow-library/bio-cwl-tools

CWL CommandLineTool descriptions for biology/life-sciences related applications

Language: Common Workflow Language - Size: 718 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 74 - Forks: 35

ga4gh/workflow-execution-service-schemas

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

Size: 4.07 MB - Last synced: about 1 month ago - Pushed: 8 months ago - Stars: 83 - Forks: 40

yuch7/cwlexec

A new open source tool to run CWL workflows on LSF

Language: Java - Size: 24 MB - Last synced: 29 days ago - Pushed: over 1 year ago - Stars: 36 - Forks: 8

stjudecloud/rfcs

Request for Comments (RFCs) on the St. Jude Cloud Project.

Language: Jupyter Notebook - Size: 4.23 MB - Last synced: about 1 month ago - Pushed: about 2 months ago - Stars: 0 - Forks: 2

EBI-Metagenomics/pipeline-v5

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

Language: HTML - Size: 376 MB - Last synced: about 1 month ago - Pushed: 10 months ago - Stars: 20 - Forks: 18

dnanexus/dxCompiler

WDL and CWL compiler for the DNAnexus platform

Language: Scala - Size: 10.9 MB - Last synced: 11 days ago - Pushed: about 2 months ago - Stars: 31 - Forks: 17

common-workflow-lab/wdl2cwl 📦

[Experimental] Workflow Definition Language (WDL) to CWL

Language: Python - Size: 179 KB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 28 - Forks: 4

NCI-GDC/gdc-dnaseq-cwl

CWL for GDC DNASeq workflows

Language: Common Workflow Language - Size: 194 MB - Last synced: about 1 month ago - Pushed: 6 months ago - Stars: 20 - Forks: 14

common-workflow-language/cwl-v1.1

Current stable CWL v1.1 specification

Language: Common Workflow Language - Size: 1.46 MB - Last synced: about 2 months ago - Pushed: 6 months ago - Stars: 6 - Forks: 11

common-workflow-language/cwlprov

Profile for provenance research object of a CWL workflow run

Size: 140 KB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 15 - Forks: 3

common-workflow-lab/wdl-cwl-translator

A translator from WDL to CWL v1.2

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

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: about 2 months ago - Pushed: 2 months ago - Stars: 12 - Forks: 3

ebi-jdispatcher/webservice-cwl-generator

Generates CWL files for Job Dispatcher Web Service Clients

Language: Python - Size: 18.6 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 1

ohsu-comp-bio/common-workflow-language Fork of common-workflow-language/common-workflow-language

Repository for CWL Specfications

Language: Web Ontology Language - Size: 2.49 MB - Last synced: 2 months ago - Pushed: almost 7 years ago - Stars: 0 - Forks: 0

nlppln/nlppln

NLP pipeline software using common workflow language

Language: Python - Size: 266 KB - Last synced: 27 days ago - Pushed: about 5 years ago - Stars: 34 - Forks: 3

ga4gh/tool-registry-service-schemas

APIs for discovering genomics tools, their metadata and their containers

Language: Shell - Size: 9.04 MB - Last synced: about 1 month ago - Pushed: 8 months ago - Stars: 30 - Forks: 18

rabix/benten

A language server for Common Workflow Language

Language: Python - Size: 5.06 MB - Last synced: 22 days ago - Pushed: 6 months ago - Stars: 66 - Forks: 10

rabix/composer

Visual and code editor for Common Workflow Language

Language: TypeScript - Size: 13.3 MB - Last synced: 15 days ago - Pushed: over 1 year ago - Stars: 298 - Forks: 74

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.

Language: Java - Size: 4.56 MB - Last synced: 3 months ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

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: 3 months ago - Pushed: over 6 years ago - Stars: 16 - Forks: 4

skoc/BCO-Execution

Repository to share data, workflows, apps, and scripts working toward the goal of execution of BioCompute Objects (BCO).

Language: Common Workflow Language - Size: 1.01 MB - Last synced: 3 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

4dn-dcic/pipelines-cwl

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

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

dockstore/dockstore-training

Working space for creating dockstore training materials

Language: wdl - Size: 103 MB - Last synced: 4 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 4

dockstore/bcc2020-training

Training materials for our BCC 2020 training workshop.

Language: Common Workflow Language - Size: 103 MB - Last synced: 4 months ago - Pushed: 7 months ago - Stars: 1 - Forks: 5

rabix/cwl-svg

A library for generating an interactive SVG visualization of CWL workflows

Language: TypeScript - Size: 10.8 MB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 76 - Forks: 18

azzaea/scalability-tst

Language: Roff - Size: 32.6 MB - Last synced: 4 months ago - Pushed: over 2 years ago - Stars: 3 - Forks: 1

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: 15 days ago - Pushed: about 1 year ago - Stars: 18 - Forks: 28

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: about 1 month ago - Pushed: over 3 years ago - Stars: 74 - Forks: 28

agduncan94/cwl_generator

A simple angular form for generating CWL tools and workflows

Language: HTML - Size: 13.7 KB - Last synced: 5 months ago - Pushed: about 7 years ago - Stars: 2 - Forks: 0

carpentries-incubator/cwl-novice-tutorial

Introduction to Workflows with Common Workflow Language

Language: HTML - Size: 5.24 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 11 - Forks: 21

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: 7 months ago - Pushed: about 5 years ago - Stars: 19 - Forks: 11

nikolapeja6/gi-proj-CNNScoreVariants

School project for the Computational Genomics (2018/2019) course, which is a part of the Master studies at the School of Electrical Engineering, University of Belgrade.

Language: Common Workflow Language - Size: 273 KB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

snap-contrib/cwl-snap-graph-runner

Process SNAP GPT graphs using docker and the Common Workflow Language (CWL)

Language: Common Workflow Language - Size: 21.5 KB - Last synced: 7 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 1

sbg/sbg_dockstore_tools

Language: Common Workflow Language - Size: 763 KB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 2 - Forks: 6

kids-first/kf-alignment-workflow

:microscope: Alignment workflow for Kids-First DRC

Language: Common Workflow Language - Size: 2.73 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 9 - Forks: 6

systemPipeR/SPblast

BLAST Workflow Template

Language: TeX - Size: 24.2 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 1

common-workflow-language/media

CWL logo source

Size: 6.38 MB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 3 - Forks: 2

common-workflow-language/governance

Holds public material generated by and for the CWL board.

Language: HTML - Size: 409 KB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 4 - Forks: 3

common-workflow-language/cwlprov-py

cwlprov: Command line tool and Python API to explore Research Objects containing provenance of Common Workflow Language executions

Language: Python - Size: 419 KB - Last synced: 25 days ago - Pushed: 10 months ago - Stars: 2 - Forks: 3

common-workflow-lab/cwl-language-server

A Language Server for CWL

Language: Python - Size: 35.2 KB - Last synced: 8 months ago - Pushed: almost 2 years ago - Stars: 3 - Forks: 2

GA4GH-DREAM/dockstore-tool-synapse-submit

Language: Shell - Size: 23.4 KB - Last synced: 9 months ago - Pushed: almost 7 years ago - Stars: 1 - Forks: 0

labbcb/workflows

Reproducible Workflows for Genomics Research

Language: wdl - Size: 191 KB - Last synced: 9 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 1

stevekm/minio-workflow-demo

Demo for using MinIO object store with Nextflow and CWL workflows

Language: Makefile - Size: 287 KB - Last synced: 8 days ago - Pushed: about 3 years ago - Stars: 4 - Forks: 0

ICGC-TCGA-PanCancer/pcawg-snv-indel-annotation

This workflow performs annotation on SNV and INDEL VCFs.

Language: JavaScript - Size: 127 KB - Last synced: 9 months ago - Pushed: over 6 years ago - Stars: 4 - Forks: 0

ICGC-TCGA-PanCancer/pcawg-oxog-filter

The CWL workflow to execute the OxoG filter.

Language: Python - Size: 30.3 KB - Last synced: 9 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

ICGC-TCGA-PanCancer/pcawg-minibam

Language: JavaScript - Size: 146 KB - Last synced: 9 months ago - Pushed: over 5 years ago - Stars: 1 - Forks: 2

ICGC-TCGA-PanCancer/OxoG-Dockstore-Tools

A CWL version of the Seqware OxoG workflow. This repository also contains scripts and dockerfiles used by the stand-alone versions of these components.

Language: Shell - Size: 117 KB - Last synced: 9 months ago - Pushed: over 5 years ago - Stars: 4 - Forks: 6

COV-IRT/kf-rnaseq-workflow Fork of kids-first/kf-rnaseq-workflow

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

Size: 197 KB - Last synced: 10 months ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

COV-IRT/d3b-dev-rnaseq-snv Fork of d3b-center/d3b-dev-rnaseq-snv

RNAseq SNV Calling Workflow (beta)

Language: Common Workflow Language - Size: 207 KB - Last synced: 10 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

anton-khodak/wdl2cwl Fork of common-workflow-lab/wdl2cwl

Convert Workflow Definiton Language (WDL) to CWL

Language: Python - Size: 22.5 KB - Last synced: 10 months ago - Pushed: over 7 years ago - Stars: 2 - Forks: 0

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

Language: JavaScript - Size: 7.81 KB - Last synced: 10 months ago - Pushed: over 5 years ago - Stars: 2 - Forks: 0

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: 10 months ago - Pushed: over 1 year ago - Stars: 15 - Forks: 5

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: 10 months ago - Pushed: over 3 years ago - Stars: 4 - Forks: 3

yyoshiaki/VIRTUS

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

Language: Common Workflow Language - Size: 9.62 MB - Last synced: 7 months ago - Pushed: about 2 years ago - Stars: 32 - Forks: 8

tom-tan/drill-hawk

A visualizer of workflow execution records for CWL

Language: HTML - Size: 10.5 MB - Last synced: 10 months ago - Pushed: about 3 years ago - Stars: 3 - Forks: 0