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: 3 days ago - Pushed at: 3 days ago - Stars: 909 - Forks: 242

eoap/machine-learning-process

Machine Learning Process using the EO Application Package

Language: Jupyter Notebook - Size: 124 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 1

fairagro/m4.4_sciwin_client

🦀 SciWIn Client: Reproducible computational Workflows made easy!

Language: Rust - Size: 1.52 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 5 - Forks: 0

Terradue/pycalrissian

Python client for Calrissian - CWL on kubernetes

Language: Python - Size: 818 KB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 3 - Forks: 5

common-workflow-language/cwltool

Common Workflow Language reference implementation

Language: Python - Size: 11.3 MB - Last synced at: about 17 hours ago - Pushed at: 13 days ago - Stars: 347 - Forks: 231

kclhi/phenoflow

Standardise and share computable disease definitions

Language: JavaScript - Size: 2.82 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 8 - Forks: 7

rabix/benten

A language server for Common Workflow Language

Language: Python - Size: 5.06 MB - Last synced at: about 22 hours ago - Pushed at: over 1 year ago - Stars: 65 - Forks: 9

common-workflow-language/cwlviewer

A web application to view and share Common Workflow Language workflows

Language: Java - Size: 10 MB - Last synced at: 14 days ago - Pushed at: 18 days 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: 2 days ago - Pushed at: over 1 year ago - Stars: 43 - Forks: 13

Barski-lab/cwl-airflow

Python package to extend Airflow functionality with CWL1.1 support

Language: Python - Size: 2.77 MB - Last synced at: about 20 hours ago - Pushed at: over 1 year ago - Stars: 187 - Forks: 32

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: 25 days ago - Pushed at: 25 days ago - Stars: 5 - Forks: 0

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: 1,463 - Forks: 195

common-workflow-language/cwl-website

www.commonwl.org

Language: JavaScript - Size: 13.5 MB - Last synced at: 14 days ago - Pushed at: about 1 month ago - Stars: 10 - Forks: 20

common-workflow-language/cwltest

Framework for testing CWL tools and workflows

Language: Python - Size: 480 KB - Last synced at: 6 days ago - Pushed at: about 1 month ago - Stars: 17 - Forks: 18

crim-ca/application-packages

OGC Application Packages using Common Workflow Language (CWL)

Language: Common Workflow Language - Size: 20.5 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

rabix/composer

Visual and code editor for Common Workflow Language

Language: TypeScript - Size: 13.3 MB - Last synced at: 29 days ago - Pushed at: over 2 years ago - Stars: 303 - Forks: 72

sbg/sevenbridges-python

SevenBridges Python Api bindings

Language: Python - Size: 1.98 MB - Last synced at: 5 days ago - Pushed at: 2 months ago - Stars: 46 - Forks: 28

sbg/sevenbridges-cwl

Seven Bridges Python library for programatic generation of CWL workflows.

Language: Python - Size: 1.3 MB - Last synced at: 4 days ago - Pushed at: over 2 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: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

yonesora56/plant2human

Analysis workflow for novel gene search based on structural similarity search

Language: Jupyter Notebook - Size: 44.1 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 4 - Forks: 0

msk-access/cwl_subworkflows

A list of subworkflows used for MSK-ACCESS data processing.

Language: Common Workflow Language - Size: 942 KB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 2 - Forks: 1

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: about 2 years ago - Stars: 49 - Forks: 19

onnovalkering/cwl-rs

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

Language: Common Workflow Language - Size: 53.7 KB - Last synced at: 9 days ago - Pushed at: over 3 years ago - Stars: 5 - Forks: 1

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: 8 days ago - Pushed at: 8 months ago - Stars: 8 - 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: 6 months ago - Pushed at: 6 months ago - Stars: 21 - Forks: 20

common-workflow-language/cwl-utils

Python utilities for CWL

Language: Python - Size: 1.38 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 36 - Forks: 18

common-workflow-language/user_guide

The CWL v1.0 - v1.2 user guide

Language: Common Workflow Language - Size: 18.3 MB - Last synced at: 7 days ago - Pushed at: 6 months ago - Stars: 42 - Forks: 68

tom-tan/conformance

Location to store the results of CWL conformance testing for ep3

Size: 253 KB - Last synced at: 25 days ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

sbg/sevenbridges-r

Seven Bridges API Client, CWL Schema, Meta Schema, and SDK Helper in R

Language: R - Size: 3.41 MB - Last synced at: 2 days ago - Pushed at: about 3 years ago - Stars: 35 - Forks: 14

tom-tan/ep3

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

Language: Ruby - Size: 386 KB - Last synced at: 6 days ago - Pushed at: about 3 years ago - Stars: 10 - Forks: 3

common-workflow-lab/upload-conformance-badges

Action for uploading CWL conformance badges

Size: 32.2 KB - Last synced at: 15 days ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

workflux/workflUX

An open-source, cloud-ready web application for simplified deployment of big data workflows.

Language: JavaScript - Size: 7.74 MB - Last synced at: 6 days ago - Pushed at: 10 months ago - Stars: 33 - Forks: 9

otiai10/cwl.go

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

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

sbg/tidycwl

Tidy Common Workflow Language Tools and Workflows

Language: Common Workflow Language - Size: 942 KB - Last synced at: 3 days ago - Pushed at: 11 months ago - Stars: 9 - Forks: 2

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: 95.2 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 22 - Forks: 5

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

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 at: over 1 year ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

sbg/bco-app

BCO App by Seven Bridges

Language: R - Size: 58.7 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 4

otiai10/yacle

Yet Another CWL Engine by Golang

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

rabix/cwl-format

A very opinionated code formatter for CWL

Language: Common Workflow Language - Size: 202 KB - Last synced at: about 20 hours ago - Pushed at: over 1 year ago - Stars: 9 - Forks: 4

giannisdoukas/ipython2cwl-demo

IPython2CWL Demo

Language: Jupyter Notebook - Size: 116 KB - Last synced at: 25 days ago - Pushed at: almost 5 years ago - Stars: 2 - Forks: 0

giannisdoukas/CWLJNIKernel

Jupyter Notebook Kernel for Common Workflow Language

Language: Python - Size: 1.67 MB - Last synced at: 1 day ago - Pushed at: over 3 years ago - Stars: 4 - Forks: 3

tom-tan/core-wire

A tool/library to make CWL engines connected to remote resources

Language: D - Size: 107 KB - Last synced at: 25 days ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

tom-tan/zatsu-cwl-generator

Simple CWL document generator from given execution commands

Language: D - Size: 119 KB - Last synced at: 25 days ago - Pushed at: over 2 years ago - Stars: 4 - 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 at: 9 months ago - Pushed at: over 2 years ago - Stars: 15 - Forks: 5

tom-tan/cwl-mode

CWL mode for Emacs

Language: Emacs Lisp - Size: 22.5 KB - Last synced at: 6 days ago - Pushed at: almost 4 years ago - Stars: 7 - Forks: 1

common-workflow-lab/cwl-language-server

A Language Server for CWL

Language: Python - Size: 35.2 KB - Last synced at: 9 months ago - Pushed at: almost 3 years ago - Stars: 3 - Forks: 2

common-workflow-lab/run-conformance-tests

Action for running CWL conformance tests

Size: 29.3 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

common-workflow-lab/run-tests

Action for running tests for CWL workflows

Size: 21.5 KB - Last synced at: about 1 month ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

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: 6 days ago - Pushed at: about 3 years ago - Stars: 7 - Forks: 2

suecharo/cwl-inputs-parser

A library for parsing the inputs field of Common Workflow Language (CWL) document.

Language: Common Workflow Language - Size: 632 KB - Last synced at: about 12 hours ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

suecharo/genpei

An implementation of GA4GH Workflow Execution Service Standard as a microservice.

Language: Python - Size: 3.65 MB - Last synced at: about 3 hours ago - Pushed at: almost 5 years ago - Stars: 8 - Forks: 1

tom-tan/drill-hawk

A visualizer of workflow execution records for CWL

Language: HTML - Size: 10.5 MB - Last synced at: 25 days ago - Pushed at: about 4 years ago - Stars: 3 - Forks: 0

suecharo/agodashi

An API server for parsing workflows written in workflow languages.

Language: Python - Size: 63.5 KB - Last synced at: 2 days ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

ktaletsk/cwl-examples

Language: Common Workflow Language - Size: 6.84 KB - Last synced at: about 2 months ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

nanxstats/sbpack-r

An R package to pack and upload CWL apps to Seven Bridges powered platforms

Language: R - Size: 48.8 KB - Last synced at: 2 days ago - Pushed at: almost 5 years ago - Stars: 1 - Forks: 0

nanxstats/cwl-exploder

Shiny app to unpack monolithic CWL workflows

Language: R - Size: 1.07 MB - Last synced at: 2 days ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

nanxstats/cwl-upgrader

Shiny app to upgrade Common Workflow Language (CWL) apps from sbg:draft2 to v1.0

Language: R - Size: 1.47 MB - Last synced at: 2 days ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

nanxstats/cwl-formatter

Shiny app to format Common Workflow Language (CWL) apps

Language: R - Size: 1.04 MB - Last synced at: 2 days ago - Pushed at: almost 5 years ago - Stars: 1 - Forks: 0

tom-tan/flycheck-cwl

Add on-the-fly checker for Common Workflow Language

Language: Emacs Lisp - Size: 3.91 KB - Last synced at: 25 days ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 0

tom-tan/cwl-conformance-test-summarizer

Summarize the result of conformance test using cwltest

Language: Ruby - Size: 6.84 KB - Last synced at: 25 days ago - Pushed at: almost 7 years ago - Stars: 3 - Forks: 0

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

stain/cwlprov-paper-gigascience

CWLProv paper submitted for GigaScience

Language: TeX - Size: 7.71 MB - Last synced at: 12 days ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0

suzuki-shm/fastANI-in-cwl

Wrapper tool of fastANI by CWL and Docker

Language: Common Workflow Language - Size: 1.1 MB - Last synced at: about 1 month ago - Pushed at: almost 6 years ago - Stars: 1 - Forks: 0

andrewjesaitis/cwl-tutorial

Tutorial for the Common Workflow Language using SnpEff

Language: Common Workflow Language - Size: 50.8 KB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 4 - Forks: 3

wtsi-hgi/cwl-dummy

Generates CWL files that do nothing.

Language: Python - Size: 57.6 KB - Last synced at: about 1 month ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0