dockstore/dockstore

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

Language: Java - Size: 40.9 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 131 - Forks: 29

EBI-Metagenomics/emg-viral-pipeline

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

Language: Python - Size: 31 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 141 - Forks: 21

common-workflow-language/cwltest

Framework for testing CWL tools and workflows

Language: Python - Size: 486 KB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 17 - Forks: 18

common-workflow-language/cwl-utils

Python utilities for CWL

Language: Python - Size: 1.76 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 40 - Forks: 20

common-workflow-language/user_guide

The CWL v1.0 - v1.2 user guide

Language: Common Workflow Language - Size: 18.5 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 43 - Forks: 66

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: 2 days ago - Pushed at: 9 months ago - Stars: 1,470 - Forks: 196

arvados/arvados

An open source platform for managing and analyzing biomedical big data

Language: Go - Size: 81.8 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 408 - Forks: 124

Duke-GCB/calrissian

CWL on Kubernetes

Language: Python - Size: 1.04 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 49 - Forks: 19

stjudecloud/workflows

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

Language: WDL - Size: 85.2 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 37 - Forks: 12

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: 96.2 MB - Last synced at: 1 day ago - Pushed at: 4 days ago - Stars: 28 - Forks: 6

parham-membari-terradue/ogc-api-processes-with-zoo Fork of eoap/ogc-api-processes-with-zoo

OGC API Processes with ZOO Project

Language: Jupyter Notebook - Size: 1.85 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 0 - Forks: 0

ga4gh/tool-registry-service-schemas

APIs for discovering genomics tools, their metadata and their containers

Language: Shell - Size: 8.2 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 31 - Forks: 18

dnanexus/dxCompiler

WDL and CWL compiler for the DNAnexus platform

Language: Scala - Size: 10.9 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 34 - Forks: 18

ga4gh/workflow-execution-service-schemas

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

Size: 4.4 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 85 - Forks: 38

common-workflow-language/cwl-website

www.commonwl.org

Language: JavaScript - Size: 13.5 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 10 - Forks: 20

eoap/cwl2ogc

CWL Worflow inputs/outputs to OGC API Processes inputs/outputs

Language: Python - Size: 976 KB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 4 - Forks: 1

aldbr/dirac-cwl-proto

Proof of Concept: integrating CWL into Dirac

Language: Python - Size: 948 KB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 0 - Forks: 1

common-workflow-language/cwlviewer

A web application to view and share Common Workflow Language workflows

Language: Java - Size: 10.1 MB - Last synced at: 4 days ago - Pushed at: 9 days ago - Stars: 47 - Forks: 29

MaayanLab/Playbook-Workflow-Builder

A repository for the Playbook Workflow Builder project.

Language: TypeScript - Size: 20.8 MB - Last synced at: 10 days ago - Pushed at: 11 days ago - Stars: 22 - Forks: 19

DataBiosphere/toil

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

Language: Python - Size: 34.6 MB - Last synced at: 3 days ago - Pushed at: 9 days ago - Stars: 915 - Forks: 245

fairagro/m4.4_sciwin_client

🦀 SciWIn Client: Reproducible computational Workflows made easy!

Language: Rust - Size: 2.81 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 8 - Forks: 2

dockstore/dockstore-ui2

Website user interface for Dockstore in Angular2

Language: TypeScript - Size: 43.1 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 17 - Forks: 16

arunisaac/ravanan

High-reproducibility CWL runner powered by Guix

Language: Scheme - Size: 951 KB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 13 - Forks: 1

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: 8 days ago - Pushed at: almost 2 years ago - Stars: 44 - Forks: 13

reanahub/reana

REANA: Reusable research data analysis platform

Language: Python - Size: 2.91 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 131 - Forks: 60

common-workflow-language/cwltool

Common Workflow Language reference implementation

Language: Python - Size: 11.2 MB - Last synced at: 7 days ago - Pushed at: 19 days ago - Stars: 351 - Forks: 233

common-workflow-language/cwljava

Java SDK for the Common Workflow Language standards

Language: Java - Size: 10.8 MB - Last synced at: 19 days ago - Pushed at: 20 days ago - Stars: 14 - Forks: 8

Terradue/cwl2puml

CWL Worflows processor to generate PlantUML diagrams

Language: Python - Size: 820 KB - Last synced at: 17 days ago - Pushed at: 23 days ago - Stars: 0 - Forks: 0

Terradue/cwl-loader

Simple utilities to load CWL documents in a transparent way

Language: Python - Size: 770 KB - Last synced at: 17 days ago - Pushed at: 23 days ago - Stars: 1 - Forks: 0

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: 26 days ago - Pushed at: 26 days ago - Stars: 27 - Forks: 7

onnovalkering/cwl

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

Language: Common Workflow Language - Size: 53.7 KB - Last synced at: 16 days ago - Pushed at: about 4 years ago - Stars: 5 - Forks: 1

kids-first/kf-alignment-workflow

:microscope: Alignment workflow for Kids-First DRC

Language: Common Workflow Language - Size: 2.78 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 11 - Forks: 6

ResearchObject/ro-crate-py

Python library for RO-Crate

Language: Python - Size: 1.05 MB - Last synced at: 2 days ago - Pushed at: about 1 month ago - Stars: 69 - Forks: 32

rabix/composer

Visual and code editor for Common Workflow Language

Language: TypeScript - Size: 13.3 MB - Last synced at: about 1 month ago - Pushed at: over 2 years ago - Stars: 306 - Forks: 72

workflowhub-eu/about

Website about the project WorkflowHub

Language: HTML - Size: 5.78 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 12 - Forks: 18

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: 10.3 MB - Last synced at: 6 days ago - Pushed at: about 1 month ago - Stars: 18 - Forks: 9

rabix/cwl-svg

A library for generating an interactive SVG visualization of CWL workflows

Language: TypeScript - Size: 10.9 MB - Last synced at: 29 days ago - Pushed at: about 1 year ago - Stars: 78 - Forks: 18

dockstore/dockstore-documentation

The documentation for Dockstore.org

Language: Shell - Size: 67.7 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 7

fairagro/m4.4_sciwin_client_examples

Example Projects for SciWIn Client

Size: 2.93 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

ResearchObject/workflow-run-crate

Workflow Run RO-Crate profile

Language: Python - Size: 56.7 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 10 - Forks: 10

NCI-GDC/aliquot-maf-cwl

CWL tools and workflows for generating and processing aliquot-MAF

Language: Common Workflow Language - Size: 63.5 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 2

NCI-GDC/muse-cwl

CWL for GDC MuSE

Language: Common Workflow Language - Size: 3.2 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 1

kids-first/kf-rnaseq-workflow

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

Language: Common Workflow Language - Size: 1.43 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 11 - Forks: 9

rabix/cwl-format

A very opinionated code formatter for CWL

Language: Common Workflow Language - Size: 204 KB - Last synced at: 17 days ago - Pushed at: 26 days ago - Stars: 10 - Forks: 4

datirium/workflows

CWL based Bioinformatics Workflows

Language: Common Workflow Language - Size: 3.88 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 17 - Forks: 18

NCI-GDC/gdc-rnaseq-cwl

GDC RNA-Seq STAR 2-Pass Workflow

Language: Common Workflow Language - Size: 16.3 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 4 - Forks: 8

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: 18 days ago - Pushed at: over 3 years ago - Stars: 6 - Forks: 5

NCI-GDC/samtools-mpileup-cwl

CWL for GDC samtools mpileup

Language: Common Workflow Language - Size: 19.5 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 1

NCI-GDC/mutect2-cwl

CWL for GDC GATK3 MuTect2

Language: Common Workflow Language - Size: 96.7 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 3

NCI-GDC/variant-filtration-cwl

Workflows for filtering GDC VCFs

Language: Common Workflow Language - Size: 208 KB - Last synced at: 16 days ago - Pushed at: 2 months ago - Stars: 1 - Forks: 2

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 at: 2 days ago - Pushed at: 3 days ago - Stars: 69 - Forks: 28

workflow-library/gdc-uploader

CWL Description of GDC Uploader

Language: Python - Size: 521 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

NCI-GDC/gatk4_mutect2_cwl

Language: Common Workflow Language - Size: 117 KB - Last synced at: 3 days ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

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: 350 MB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 23 - Forks: 2

nlppln/nlppln

NLP pipeline software using common workflow language

Language: Python - Size: 266 KB - Last synced at: 2 days ago - Pushed at: over 6 years ago - Stars: 34 - Forks: 3

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: 4 months ago - Pushed at: over 1 year ago - Stars: 188 - Forks: 65

Barski-lab/cwl-airflow

Python package to extend Airflow functionality with CWL1.1 support

Language: Python - Size: 2.77 MB - Last synced at: 11 days ago - Pushed at: almost 2 years ago - Stars: 188 - Forks: 32

Terradue/pycalrissian

Python client for Calrissian - CWL on kubernetes

Language: Python - Size: 863 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 3 - Forks: 5

rabix/benten

A language server for Common Workflow Language

Language: Python - Size: 5.06 MB - Last synced at: 15 days ago - Pushed at: almost 2 years ago - Stars: 65 - Forks: 9

eoap/ogc-api-processes-with-zoo

OGC API Processes with ZOO Project

Language: Jupyter Notebook - Size: 3.39 MB - Last synced at: 29 days ago - Pushed at: 29 days ago - Stars: 0 - Forks: 2

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: 5 months ago - Pushed at: 5 months ago - Stars: 5 - Forks: 0

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: 6 months ago - Pushed at: 6 months ago - Stars: 78 - Forks: 38

NCI-GDC/vep-cwl

GDC VEP Variant Annotation Workflow

Language: Common Workflow Language - Size: 134 KB - Last synced at: 3 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 3

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: about 1 month ago - Pushed at: over 6 years ago - Stars: 19 - Forks: 12

crim-ca/application-packages

OGC Application Packages using Common Workflow Language (CWL)

Language: Common Workflow Language - Size: 20.5 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

Template-Latex/cwl-docs

Archivos autocompletado .cwl para Template-Latex

Language: Common Workflow Language - Size: 57.6 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 2 - Forks: 0

kids-first/kf-somatic-workflow

:microscope: Somatic workflow for Kids-First

Language: Common Workflow Language - Size: 8.44 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 13 - Forks: 2

stjudecloud/rfcs

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

Language: Jupyter Notebook - Size: 4.73 MB - Last synced at: 5 months ago - Pushed at: 8 months ago - Stars: 1 - Forks: 2

sbg/sevenbridges-cwl

Seven Bridges Python library for programatic generation of CWL workflows.

Language: Python - Size: 1.3 MB - Last synced at: 15 days ago - Pushed at: almost 3 years ago - Stars: 20 - Forks: 3

davidroberson/generative-cwl

Generative CWL: Less Boilerplate, More Science

Language: Common Workflow Language - Size: 89.8 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

NCI-GDC/gdc-mirnaseq-cwl

CWL workflows and tools for the miRNA-Seq workflow

Language: Common Workflow Language - Size: 174 KB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 1

common-workflow-language/cwl-upgrader

Upgrade CWL syntax to a newer version

Language: Python - Size: 230 KB - Last synced at: 19 days ago - Pushed at: 26 days ago - Stars: 5 - Forks: 3

rabix/cwl-ts

Typescript data model for Common Workflow Language

Language: TypeScript - Size: 2.49 MB - Last synced at: about 1 month ago - Pushed at: over 2 years ago - Stars: 49 - Forks: 19

fabricebrito/dev-platform-calrissian

Bootstraps a kubernetes environment to run CWL documents with Calrissian

Language: Dockerfile - Size: 5.86 KB - Last synced at: 6 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

rosafilgueira/Workflows_Seminar

Exploring Scientific Workflows with CWL and dispel4py

Language: Jupyter Notebook - Size: 27.5 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 2 - Forks: 0

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: 2 months ago - Pushed at: about 1 year ago - Stars: 8 - Forks: 3

NCI-GDC/gdc-dnaseq-cwl

CWL for GDC DNASeq workflows

Language: Common Workflow Language - Size: 194 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 22 - Forks: 14

common-workflow-language/media

CWL logo source

Size: 6.38 MB - Last synced at: 5 months ago - Pushed at: over 3 years ago - Stars: 4 - Forks: 2

common-workflow-lab/cwl-d-auto

Autogenerated classes for reading and writing CWL objects using the D language

Language: Common Workflow Language - Size: 339 KB - Last synced at: 6 months ago - Pushed at: 11 months ago - Stars: 3 - Forks: 0

datirium/scidap

Scientific Data Analysis Platform

Size: 376 KB - Last synced at: 6 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 3

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: 11 months ago - Pushed at: 11 months ago - Stars: 21 - Forks: 20

BerndDoser/ML-workflow-orchestration

Seminar: Machine Learning Workflow Orchestration

Language: Common Workflow Language - Size: 8.43 MB - Last synced at: about 1 month ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

yyoshiaki/VIRTUS

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

Language: Common Workflow Language - Size: 9.62 MB - Last synced at: 6 months ago - Pushed at: over 3 years ago - Stars: 34 - Forks: 9

kids-first/kf-jointgenotyping-workflow

:microscope: Joint genotyping workflow for Kids-First DRC

Language: Common Workflow Language - Size: 2.15 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 6 - Forks: 1

rworkflow/RcwlRecipes

Language: Common Workflow Language - Size: 667 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 2 - Forks: 3

msk-access/uncollapsed_bam_generation

Workflow for making MSK-ACCESS standard binary alignment mapping file.

Language: Common Workflow Language - Size: 1.83 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 2

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 at: 4 days ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 3

tom-tan/conformance

Location to store the results of CWL conformance testing for ep3

Size: 253 KB - Last synced at: 5 months ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

common-workflow-language/cwl-v1.1

Current stable CWL v1.1 specification

Language: Common Workflow Language - Size: 1.46 MB - Last synced at: 1 day ago - Pushed at: 9 months ago - Stars: 7 - Forks: 11

common-workflow-language/cwlprov

Profile for provenance research object of a CWL workflow run

Size: 140 KB - Last synced at: 5 months ago - Pushed at: over 2 years ago - Stars: 17 - Forks: 3

mwiens91/hello-world-workflow

A tiny test CWL workflow to help develop new features for Toil

Language: Common Workflow Language - Size: 16.6 KB - Last synced at: about 1 year ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0

buchanae/cwl

common workflow language library and runtime

Language: Go - Size: 274 KB - Last synced at: 5 months ago - Pushed at: over 6 years ago - Stars: 7 - Forks: 3

tom-tan/ep3

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

Language: Ruby - Size: 386 KB - Last synced at: 5 months ago - Pushed at: over 3 years ago - Stars: 10 - Forks: 3

Consonance/consonance

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

Language: Java - Size: 3.81 MB - Last synced at: 6 months ago - Pushed at: about 7 years ago - Stars: 14 - Forks: 5

common-workflow-lab/upload-conformance-badges

Action for uploading CWL conformance badges

Size: 32.2 KB - Last synced at: 27 days ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

otiai10/cwl.go

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

Language: Go - Size: 582 KB - Last synced at: 25 days ago - Pushed at: over 6 years ago - Stars: 22 - Forks: 7

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: 6 months ago - Pushed at: about 5 years ago - Stars: 5 - Forks: 3

common-workflow-language/governance

Holds public material generated by and for the CWL board.

Language: HTML - Size: 412 KB - Last synced at: 5 months ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 3

umccr/cwl-novice-tutorial

CWL Novice Tutorial

Language: HTML - Size: 11.5 MB - Last synced at: 6 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

rworkflow/Rcwl

Write CWL in R

Language: R - Size: 2.49 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 13 - Forks: 4