wdl

There are 3 repositories under wdl topic.

cromwell
broadinstitute / cromwell
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
workflow-execution workflow cloud hpc bioinformatics executor scala docker ga4gh containers wdl workflow-description-language application
Language:Scala 957
DataBiosphere / toil
A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.
cwl python mesos slurm gridengine workflow pipeline aws common-workflow-language kubernetes wdl
Language:Python 869
openwdl / wdl
Workflow Description Language - Specification and Implementations
wdl workflow cromwell bioinformatics reproducible-science reproducibility cloud openwdl
724
reapack
cfillion / reapack
📦 Package manager for REAPER
reaper reapack wdl reaper-plugin package-manager
Language:C++ 300
chanzuckerberg / miniwdl
Workflow Description Language developer tools & local runner
wdl workflow-description-language
Language:Python 167
broadinstitute / long-read-pipelines
Long read production pipelines
pipelines wdl long-reads de-novo-assembly variant-calling
Language:Jupyter Notebook 116
dockstore / dockstore
Our VM/Docker sharing infrastructure and management component
bioinformatics containers cwl docker dockstore nextflow wdl workflow
Language:Java 114
dnanexus / UKB_RAP
Access share reviewed code & Jupyter Notebooks for use on the UK Biobank (UKBB) Research Application Platform. Includes resources from DNAnexus webinars, online trainings and workshops.
ukbiobank wdl gwas
Language:Jupyter Notebook 95
ga4gh / workflow-execution-service-schemas
The WES API is a standard way to run and manage portable workflows.
cwl ga4gh wdl workflow
83
biowdl / tasks
A collection of reusable WDL tasks. Category:Other
bioinformatics bioinformatics-pipeline tasks wdl wdl-tasks workflow
Language:WDL 82
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.
pipelines aws-step-function aws docker aws-lambda bioinformatics cwl wdl cwl-workflow wdl-workflow snakemake snakemake-workflow conda
Language:Python 67
LUMC / pytest-workflow
Configure workflow/pipeline tests using yaml files.
testing test workflow pipeline pytest-plugin pytest yaml wdl cromwell snakemake workflow-testing wdl-devtools nextflow miniwdl
Language:Python 61
broadinstitute / cromshell
CLI for interacting with Cromwell servers
cromwell wdl cli bioinformatics workflow
Language:Python 52
dnanexus / dxWDL
Workflow Description Language compiler for the DNAnexus platform
wdl workflow-description-language
Language:Java 40
stjudecloud / oliver
An opinionated Cromwell orchestration manager.
genomics cromwell workflow oliver wdl workflow-execution hpc next-generation-sequencing bioinformatics bioinformatics-pipeline wdl-workflow
Language:Python 40
broadinstitute / wdl-ide
Rich IDE support for Workflow Description Language
ide wdl vscode theia cromwell docker wdl-devtools lsp
Language:Python 39
PMCC-BioinformaticsCore / janis
[Alpha] Janis: an open source tool to machine generate type-safe CWL and WDL workflows
workflow common-workflow-language workflow-description-language cwl wdl python
Language:Python 39
dnanexus / dxCompiler
WDL and CWL compiler for the DNAnexus platform
wdl cwl dnanexus compiler
Language:Scala 31
biowdl / RNA-seq
A BioWDL pipeline for processing RNA-seq data, starting with FASTQ files to produce expression measures and VCFs. Category:Multi-Sample
gatk-bestpractices gatk4 multisample pipeline rna-seq wdl
Language:wdl 30
ga4gh / tool-registry-service-schemas
APIs for discovering genomics tools, their metadata and their containers
ga4gh api tool workflow cwl wdl
Language:Shell 30
otiai10 / hotsub
Command line tool to run batch jobs concurrently with ETL framework on AWS or other cloud computing resources
workflow workflow-engine etl-framework bioinformatics cwl cwl-workflow wdl wdl-workflow batch-job aws gcp docker docker-machine
Language:Go 30
stjudecloud / workflows
Bioinformatics workflows developed for and used on the St. Jude Cloud project.
bioinformatics-workflows workflows cromwell wdl bioinformatics computational-biology workflow workflow-engine next-generation-sequencing genomics stjudecloud wdl-workflow cwl cwl-workflow
Language:WDL 30
common-workflow-lab / wdl2cwl
[Experimental] Workflow Definition Language (WDL) to CWL
commonwl cwl wdl wdl-workflow
Language:Python 28
stjudecloud / wdldoc
Create WDL documentation using Markdown.
bioinformatics genomics computational-biology workflow wdl wdl-workflow cromwell next-generation-sequencing stjudecloud
Language:Python 27
common-workflow-lab / wdl-cwl-translator
A translator from WDL to CWL v1.2
commonwl cwl wdl
Language:Common Workflow Language 26
biowdl / germline-DNA
A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample
gatk-bestpractices gatk4 germline-variants multisample pipeline somatic-variants structural-variation variantcalling wdl
Language:wdl 23
pumbaa
lmtani / pumbaa
Command-line interface for Cromwell server
cromwell cli workflow bioinformatics wdl
Language:Go 16
dockstore / dockstore-ui2
Website user interface for Dockstore in Angular2
angular cwl dockstore hacktoberfest nextflow wdl
Language:TypeScript 15
aCLImatise / CliHelpParser
Reads the output from CLI help commands, and generates machine readable schemas (CWL etc)
bioinformatics cwl wdl pipeline workflow parser cli
Language:Python 14
stjude-rust-labs / wdl
Rust crates for working with Workflow Description Language (WDL) documents.
bioinformatics next-generation-sequencing ngs wdl wdl-workflow workflow workflow-engine
Language:Rust 14
broadinstitute / widdler
A command-line tool for executing, managing, and querying WDL workflows on Cromwell servers.
cromwell wdl wdl-workflow python
Language:Python 13
biowdl / wdl-aid
Automatic Input Documentation for WDL workflows
documentation documentation-generator jinja2 wdl wdl-workflows
Language:Python 11
DaMatrix / 2b2tMapDownloader
A project to download 2b2t's map (WIP)
2b2t minecraft world-downloader wdl world-downloader-mod minecraft-mod
Language:Java 9
danishsshaikh / KCCafeteria
Project for 5th Semester Subject -> WDL & DBMS
webdevelopment canteen xampp wdl dbms php css html mysql miniproject
Language:PHP 9
ga4gh / cloud-interop-testing
Interoperable execution of workflows using GA4GH APIs
workflow cwl wdl ga4gh
Language:Python 9
truwl / capanno
cwl/wdl/sm/nf files, tool and workflow metadata, and input specifications.
cwl wdl snakemake nextflow
Language:WDL 8

wdl

broadinstitute / cromwell

DataBiosphere / toil

openwdl / wdl

cfillion / reapack

chanzuckerberg / miniwdl

broadinstitute / long-read-pipelines

dockstore / dockstore

dnanexus / UKB_RAP

ga4gh / workflow-execution-service-schemas

biowdl / tasks

4dn-dcic / tibanna

LUMC / pytest-workflow

broadinstitute / cromshell

dnanexus / dxWDL

stjudecloud / oliver

broadinstitute / wdl-ide

PMCC-BioinformaticsCore / janis

dnanexus / dxCompiler

biowdl / RNA-seq

ga4gh / tool-registry-service-schemas

otiai10 / hotsub

stjudecloud / workflows

common-workflow-lab / wdl2cwl

stjudecloud / wdldoc

common-workflow-lab / wdl-cwl-translator

biowdl / germline-DNA

lmtani / pumbaa

dockstore / dockstore-ui2

aCLImatise / CliHelpParser

stjude-rust-labs / wdl

broadinstitute / widdler

biowdl / wdl-aid

DaMatrix / 2b2tMapDownloader

danishsshaikh / KCCafeteria

ga4gh / cloud-interop-testing

truwl / capanno