Common Workflow Language | Ecosyste.ms: Awesome

https://github.com/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

Last synced: 05 Dec 2024

https://github.com/DataBiosphere/toil

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

aws common-workflow-language cwl gridengine kubernetes mesos pipeline python slurm wdl workflow workflow-description-language

Last synced: 06 Nov 2024

https://github.com/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

Last synced: 20 Dec 2024

https://github.com/common-workflow-language/cwltool

Common Workflow Language reference implementation

common-workflow-language commonwl containers cwl science sciworkflows workflows

Last synced: 19 Dec 2024

https://github.com/Barski-lab/cwl-airflow

Python package to extend Airflow functionality with CWL1.1 support

common-workflow-language commonwl containers cwl cwl-airflow cwl-descriptor dag workflow

Last synced: 25 Nov 2024

https://github.com/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

analytics cancer cancer-imaging-research cbica cpp cpp11 cwl cwltool image-analysis itcr machine-learning medical-image-computing medical-image-processing medical-imaging nci nci-itcr nih radiomics radiomics-features u24

Last synced: 14 Nov 2024

https://github.com/EBI-Metagenomics/emg-viral-pipeline

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

cwl nextflow pipeline viruses workflow

Last synced: 16 Nov 2024

https://github.com/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.

aws aws-lambda aws-step-function bioinformatics conda cwl cwl-workflow docker pipelines snakemake snakemake-workflow wdl wdl-workflow

Last synced: 08 Nov 2024

https://github.com/common-workflow-language/cwlviewer

A web application to view and share Common Workflow Language workflows

common-workflow-language cwl java workflow workflows

Last synced: 19 Dec 2024

https://github.com/Duke-GCB/calrissian

CWL on Kubernetes

cwl cwl-workflow cwl-workflows kubernetes

Last synced: 23 Oct 2024

https://github.com/common-workflow-language/user_guide

The CWL v1.0 - v1.2 user guide

common-workflow-language cwl workflow workflows

Last synced: 19 Dec 2024

https://github.com/NLeSC/scriptcwl

Create cwl workflows by writing a simple Python script

cwl python workflow

Last synced: 23 Oct 2024

https://github.com/common-workflow-language/cwl-utils

Python utilities for CWL

common-workflow-language commonwl cwl

Last synced: 19 Dec 2024

https://github.com/nlppln/nlppln

NLP pipeline software using common workflow language

cwl nlp pipeline text-mining workflow

Last synced: 23 Oct 2024

https://github.com/stjudecloud/workflows

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

bioinformatics bioinformatics-workflows computational-biology cromwell cwl cwl-workflow genomics next-generation-sequencing stjudecloud wdl wdl-workflow workflow workflow-engine workflows

Last synced: 21 Nov 2024

https://github.com/yyoshiaki/VIRTUS

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

cwl rnaseq virus-detection

Last synced: 23 Oct 2024

https://github.com/otiai10/hotsub

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

aws batch-job bioinformatics cwl cwl-workflow docker docker-machine etl-framework gcp wdl wdl-workflow workflow workflow-engine

Last synced: 08 Nov 2024

https://github.com/ga4gh/tool-registry-service-schemas

APIs for discovering genomics tools, their metadata and their containers

api cwl ga4gh tool wdl workflow

Last synced: 23 Oct 2024

https://github.com/otiai10/cwl.go

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

bioinformatics common-workflow-language cwl golang

Last synced: 08 Nov 2024

https://github.com/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.

aws bioinformatics bioinformatics-pipeline budgeting cwl ec2 ephemeral genomic-data-analysis giab human-genome informatics ngs parallel-cluster scalable scaling slurm snakemake snv-call wgs

Last synced: 15 Nov 2024

https://github.com/otiai10/yacle

Yet Another CWL Engine by Golang

bioinformatics common-workflow-language cwl

Last synced: 16 Oct 2024

https://github.com/common-workflow-language/cwlprov

Profile for provenance research object of a CWL workflow run

bagit cwl cwlprov linked-data prov provenance rdf research-object workflow

Last synced: 19 Dec 2024

https://github.com/common-workflow-language/cwltest

Framework for testing CWL tools and workflows

common-workflow-language cwl

Last synced: 19 Dec 2024

https://github.com/antonjan/Raspberry_Telemetry

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

afsk aprs ax25 balloon command cwl direwolf satellite sdr telemetry transponder

Last synced: 06 Nov 2024

https://github.com/Consonance/consonance

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

aws-ec2 azure cloud cwl java openstack

Last synced: 23 Oct 2024

https://github.com/aCLImatise/CliHelpParser

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

bioinformatics cli cwl parser pipeline wdl workflow

Last synced: 23 Oct 2024

https://github.com/common-workflow-language/cwljava

Java SDK for the Common Workflow Language standards

commonwl cwl java

Last synced: 19 Dec 2024

https://github.com/maayanlab/playbook-workflow-builder

A repository for the Playbook Workflow Builder project.

bioinformatics biology cwl data-science gene-expression gene-ontology gene-sets proteomics rna-seq-analysis systems-biology workflow

Last synced: 21 Nov 2024

https://github.com/common-workflow-language/cwl-website

www.commonwl.org

common-workflow-language cwl

Last synced: 19 Dec 2024

https://github.com/kids-first/kf-rnaseq-workflow

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

bioinformatics cwl drc-harmonization

Last synced: 23 Oct 2024

https://github.com/tom-tan/ep3

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

common-workflow-language commonwl cwl workflow workflow-engine

Last synced: 15 Oct 2024

https://github.com/truwl/capanno

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

cwl nextflow snakemake wdl

Last synced: 23 Oct 2024

https://github.com/wtsi-hgi/gatk-cwl-generator

Generates CWL files from the GATK documentation

cwl gatk

Last synced: 28 Nov 2024

https://github.com/common-workflow-language/cwl-v1.1

Current stable CWL v1.1 specification

cwl workflow

Last synced: 19 Dec 2024

https://github.com/tom-tan/cwl-template-for-vscode

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

common-workflow-language commonwl cwl template vscode

Last synced: 05 Dec 2024

https://github.com/tom-tan/cwl-inspector

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

common-workflow-language cwl

Last synced: 15 Oct 2024

https://github.com/common-workflow-language/cwl-upgrader

Upgrade CWL syntax to a newer version

commonwl cwl

Last synced: 19 Dec 2024

https://github.com/ICGC-TCGA-PanCancer/pcawg-snv-indel-annotation

This workflow performs annotation on SNV and INDEL VCFs.

cwl cwl-workflow indel-annotation pcawg snv-annotation

Last synced: 23 Oct 2024

https://github.com/tom-tan/zatsu-cwl-generator

Simple CWL document generator from given execution commands

common-workflow-language commonwl cwl dlang

Last synced: 05 Dec 2024

https://github.com/common-workflow-language/governance

Holds public material generated by and for the CWL board.

cwl

Last synced: 19 Dec 2024

https://github.com/onnovalkering/cwl-rs

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

common-workflow-language cwl

Last synced: 23 Oct 2024

https://github.com/workflowhub-eu/galaxy2cwl

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

biohackcovid20 cwl galaxy galaxy-workflows ro-crate workflow workflowhub

Last synced: 23 Oct 2024

https://github.com/NAL-i5K/Organism_Onboarding

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

cwl pipeline

Last synced: 23 Oct 2024

https://gitlab.com/m-unlock/cwl

Common Workflow Language - computational workflows

bioinformatics cwl pipelines

Last synced: 23 Oct 2024

https://github.com/xenon-middleware/xenonflow

Run CWL workflows using Xenon through a REST api

cwl java workflow xenon

Last synced: 23 Oct 2024

https://github.com/giannisdoukas/cwljnikernel

Jupyter Notebook Kernel for Common Workflow Language

common-workflow-language cwl jupyter-notebook workflows

Last synced: 06 Nov 2024

https://github.com/common-workflow-language/cwlprov-py

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

bagit cwl prov provenance python research-object

Last synced: 19 Dec 2024

https://github.com/azzaea/scalability-tst

cwl nextflow wdl

Last synced: 23 Oct 2024

https://github.com/broadinstitute/wdl4s

Scala bindings for WDL

cwl scala wdl

Last synced: 23 Oct 2024

https://github.com/tom-tan/cwl-conformance-test-summarizer

Summarize the result of conformance test using cwltest

common-workflow-language conformance-tests cwl

Last synced: 05 Dec 2024

https://github.com/tom-tan/drill-hawk

A visualizer of workflow execution records for CWL

common-workflow-language commonwl cwl visualizer

Last synced: 05 Dec 2024

https://github.com/common-workflow-language/media

CWL logo source

cwl

Last synced: 19 Dec 2024

https://github.com/seanpm2001/Learn-CommonWorkflowLanguage

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

article commonworkflowlanguage cwl cwl-lang cwl-language gpl3 gplv3 knowledge learn learn-cwl learn-cwl-lang learn-cwl-language md seanpm2001 seanpm2001-education seanpm2001-learn txt

Last synced: 23 Oct 2024

https://github.com/Template-Latex/cwl-docs

Archivos autocompletado .cwl para Template-Latex

cwl latex template template-latex

Last synced: 23 Oct 2024

https://github.com/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

cwl

Last synced: 21 Dec 2024

https://github.com/NLeSC/pycwl

Python Library for CWL

cwl python sdk

Last synced: 23 Oct 2024

https://github.com/anton-khodak/wdl2cwl

Convert Workflow Definiton Language (WDL) to CWL

cwl wdl wip

Last synced: 23 Oct 2024

https://github.com/wtsi-hgi/cwl-graph-generate

Generates https://view.commonwl.org/ like workflows images, showing a complete workflow.

cwl graph image-generation

Last synced: 28 Nov 2024

https://github.com/giannisdoukas/ipython2cwl-demo

IPython2CWL Demo

common-workflow-language cwl jupyter-notebook

Last synced: 06 Dec 2024

https://github.com/common-workflow-lab/cwl-d-auto

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

commonwl cwl dlang parser

Last synced: 23 Oct 2024

https://github.com/r78v10a07/RNASeqWF

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

cwl jupyter-notebook rnaseq

Last synced: 23 Oct 2024

https://github.com/cwl-for-eo/guide

Guide with best practices and examples to adopt CWL in Earth Observation workflows

cwl earth-observation earth-science gdal orfeotoolbox otb snap

Last synced: 23 Oct 2024

https://github.com/nanxstats/cwl-formatter

Shiny app to format Common Workflow Language (CWL) apps

bioinformatics code-formatter common-workflow-language cwl reticulate shiny-apps

Last synced: 16 Nov 2024

https://github.com/hisplan/vagrant-ubuntu-singularity-cwl

cwl singularity vagrant

Last synced: 23 Oct 2024

https://github.com/manabuishii/cwl-samples

CWL samples

cwl

Last synced: 05 Dec 2024

https://github.com/nanxstats/sbpack-r

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

bioinformatics common-workflow-language cwl reticulate

Last synced: 16 Nov 2024

https://github.com/suzuki-shm/fastANI-in-cwl

Wrapper tool of fastANI by CWL and Docker

bioinformatics common-workflow-language cwl genome

Last synced: 23 Oct 2024

https://github.com/NLeSC/cwl-tutorial

Simple CWL tutorial based on the gentle introduction to CWL

cwl tutorial

Last synced: 23 Oct 2024

https://github.com/kids-first/kf-genotype-refinement-workflow

bioinformatics cwl

Last synced: 23 Oct 2024

https://github.com/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.

clan-war-league clash-of-clans clashofclans coc cwl java player-ranking

Last synced: 23 Oct 2024

https://github.com/NCI-GDC/varscan-cwl

CWL for GDC VarScan2

bioinformatics cwl workflow

Last synced: 23 Oct 2024

https://github.com/fpsom/intro-to-cwl-docker

Introduction to CWL and Docker

cwl docker training

Last synced: 23 Oct 2024

https://github.com/Terradue/ogc-eo-application-package-hands-on

OGC EO Application Package Hands-on

cwl cwl-workflow earth-observation eo python sentinel-2

Last synced: 23 Oct 2024

https://github.com/NCI-GDC/gdc-sanger-somatic-cwl

CWL Workflows for the Sanger Somatic Workflow

bioinformatics cwl workflow

Last synced: 23 Oct 2024

https://github.com/GusEllerm/GIS_IndexGen

Prototype implementation of LivePaper with GIS indices as the subject.

cwl cwl-workflow gis livedata livepaper remote-sensing

Last synced: 23 Oct 2024

https://github.com/emulation-as-a-service/cwl-rewriter

cwl experiment

Last synced: 23 Oct 2024

https://github.com/inab/vre_wfexs_executor

WfExS tool job executor for VRE (under development)

cwl nextflow ro-crate tool vre wfexs wrapper

Last synced: 10 Nov 2024

https://github.com/inab/ipc_workflows

iPC Workflows for VRE

cwl ipc ipc-project nextflow singularity vre workflows

Last synced: 10 Nov 2024

https://github.com/dockstore/dockstore-training

Working space for creating dockstore training materials

cwl docker nextflow wdl

Last synced: 23 Oct 2024

https://github.com/umccr/cwl-novice-tutorial

CWL Novice Tutorial

cwl

Last synced: 23 Oct 2024

https://github.com/NCI-GDC/samtools-mpileup-cwl

CWL for GDC samtools mpileup

bioinformatics cwl workflow

Last synced: 23 Oct 2024

https://github.com/fairagro/M4.4_UC6_ARC

UC6 workflow in ARC proof-of-concept

common-workflow-language cwl fairagro

Last synced: 23 Oct 2024

https://github.com/emulation-as-a-service/cwl-action

cwl

Last synced: 23 Oct 2024

https://github.com/mattdoug604/help-to-cwl

Automatically generate a bare-bones CWL tool for your program of interest.

cwl python

Last synced: 09 Nov 2024

https://github.com/bernddoser/ml-workflow-orchestration

Seminar: Machine Learning Workflow Orchestration

cwl flyte machine-learning workflow

Last synced: 15 Dec 2024

https://github.com/nanxstats/cwl-upgrader

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

bioinformatics common-workflow-language cwl reticulate shiny-apps

Last synced: 16 Nov 2024

https://github.com/nanxstats/cwl-exploder

Shiny app to unpack monolithic CWL workflows

bioinformatics common-workflow-language cwl reticulate shiny-apps

Last synced: 16 Nov 2024

https://github.com/beroukhim-lab/GATK_CN_CWL

Implementation of the GATK copy number pipeline in CWL (ported from WDL)

cnv cwl gatk gdc wdl

Last synced: 23 Oct 2024

https://github.com/stjudecloud/rfcs

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

bioinformatics bioinformatics-pipeline computational-biology cwl cwl-workflow discussion genomics proposal rfcs stjudecloud wdl wdl-workflow workflow workflow-engine

Last synced: 21 Nov 2024

https://github.com/systemPipeR/SPblast

BLAST Workflow Template

analysis-pipeline blast cwl development systempiper systempiper-workflows workflow

Last synced: 23 Oct 2024

https://github.com/wtsi-hgi/cwl-dummy

Generates CWL files that do nothing.

common-workflow-language cwl

Last synced: 28 Nov 2024

https://github.com/COV-IRT/d3b-dev-rnaseq-snv

RNAseq SNV Calling Workflow (beta)

cwl rnaseq workflows

Last synced: 23 Oct 2024

https://github.com/tom-tan/conformance

Location to store the results of CWL conformance testing for ep3

common-workflow-language commonwl cwl

Last synced: 05 Dec 2024