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wdl
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88 search results found
Cromwell
⭐
944
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
Toil
⭐
860
A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.
Wdl
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706
Workflow Description Language - Specification and Implementations
Reapack
⭐
252
📦 Package manager for REAPER
Warp
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163
WDL Analysis Research Pipelines
Miniwdl
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160
Workflow Description Language developer tools & local runner
Dockstore
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113
Our VM/Docker sharing infrastructure and management component
Long Read Pipelines
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108
Long read production pipelines
Gatk4 Data Processing
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99
Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
Gatk4 Germline Snps Indels
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88
Workflows for germline short variant discovery with GATK4
Workflow Execution Service Schemas
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83
The WES API is a standard way to run and manage portable workflows.
Tasks
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78
A collection of reusable WDL tasks. Category:Other
Tibanna
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68
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.
Ukb_rap
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68
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.
Learn Wdl
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64
Educational materials for learning WDL
Gatk4 Somatic Snvs Indels
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54
This repo will be archived soon, these workflows will be housed in the GATK repository under the scripts directory. These workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.
Pytest Workflow
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52
Configure workflow/pipeline tests using yaml files.
Cromshell
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51
CLI for interacting with Cromwell servers
Viral Pipelines
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48
viral-ngs: complete pipelines
Cumulus
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45
Cloud-based scalable and efficient single-cell genomics workflows
Skylab
⭐
40
Soon to be deprecated in favor of broadinstitute/warp github repo. Previously: Secondary analysis pipelines
Five Dollar Genome Analysis Pipeline
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40
Workflows used for WGS data processing -- replaced by https://github.com/gatk-workflows/gatk4-genome-pro
Janis
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39
[Alpha] Janis: an open source tool to machine generate type-safe CWL and WDL workflows
Broad Prod Wgs Germline Snps Indels
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39
Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://github.com/gatk-workflows/five-dollar-geno
Gatk4 Exome Analysis Pipeline
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37
This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and Indel discovery in human exome sequencing data.
Oliver
⭐
36
An opinionated Cromwell orchestration manager.
Hic Pipeline
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34
HiC uniform processing pipeline
Dxwdl
⭐
33
Workflow Description Language compiler for the DNAnexus platform
Hifi Human Wgs Wdl
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33
Gatk3 4 Rnaseq Germline Snps Indels
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33
Workflows for processing RNA data for germline short variant discovery with GATK (v3+v4) and related tools
Public_health_viral_genomics
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32
Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, especially SARS-CoV-2
Long Read Rna Pipeline
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31
ENCODE long read RNA-seq pipeline
Tool Registry Service Schemas
⭐
30
APIs for discovering genomics tools, their metadata and their containers
Gatk4 Somatic Cnvs
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30
This repo will be archived soon, these workflows will be housed in the GATK repository under the scripts directory. These workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.
Dxcompiler
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29
WDL and CWL compiler for the DNAnexus platform
Workflows
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28
Bioinformatics workflows developed for and used on the St. Jude Cloud project.
Wdl2cwl
⭐
26
[Experimental] Workflow Definition Language (WDL) to CWL
Wdl Ide
⭐
26
Rich IDE support for Workflow Description Language
Wdldoc
⭐
26
Create WDL documentation using Markdown.
Wdl Cwl Translator
⭐
25
A translator from WDL to CWL v1.2
Public_health_bacterial_genomics
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24
Hotsub
⭐
23
Command line tool to run batch jobs concurrently with ETL framework on AWS or other cloud computing resources
Public_health_bioinformatics
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23
Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.
Germline Dna
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23
A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample
Gatk4 Rnaseq Germline Snps Indels
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22
Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools
Napu_wf
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22
WDL workflows for variant calling and assembly using ONT
Sv Pipeline
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21
Pipeline for structural variation detection in cohorts
Seq Format Conversion
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18
Workflows for converting between sequence data formats
Palantir Workflows
⭐
18
Utility workflows for the DSP hydro.gen team (formerly palantir)
Rna Seq
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18
A BioWDL pipeline for processing RNA-seq data, starting with FASTQ files to produce expression measures and VCFs. Category:Multi-Sample
Parabricks Wdl
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18
Accelerated genomics workflows in the Workflow Description Language
Finemapping Pipeline
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17
Statistical fine-mapping pipeline in FinnGen
Gatk4 Genome Processing Pipeline
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16
Workflows used for processing whole genome sequence data + germline variant calling. This Repository has been archived, please visit the link the ReadMe to obtain the latest version of the workflow.
Dockstore Ui2
⭐
15
Website user interface for Dockstore in Angular2
Pumbaa
⭐
14
Command-line interface for Cromwell server
Epi Share Seq Pipeline
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14
Epigenomics Program pipeline to analyze SHARE-seq data.
Clihelpparser
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13
Library for reading the output from CLI help commands, and generating machine readable schemas (CWL etc)
Vg_wdl
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12
Workflow Description Language (WDL) scripts for common vg workflows
Bigstack
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12
Saige Pipelines
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12
Pb Human Wgs Workflow Wdl
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11
Topmed Workflows
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10
a place for topmed workflows
Cloud Interop Testing
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9
Interoperable execution of workflows using GA4GH APIs
Capanno
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9
cwl/wdl/sm/nf files, tool and workflow metadata, and input specifications.
Facets
⭐
9
Implementation of FACETS for Terra
Snakemake_nextflow_wdl
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9
simple comparison of snakemake, nextflow and cromwell/wdl
Rna Seq
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8
bioinformatics pipelines
Gatk For Microbes
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8
Gatk4 Mitochondria Pipeline
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8
Workflow for SNP and INDEL variant calling on mitochondria.
Somatic Variantcalling
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7
A pipeline for somatic variantcalling. Category:Single-Sample
Mignon
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7
Mechanistic integrative analysis of RNA-Seq data
Mirna Seq Pipeline
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7
C Bird
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7
🦠 Bacterial Identification and Antimicrobial Resistance 💊
Structural Variantcalling
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7
A workflow for calling structural variants. Category:Single-Sample
Rna Seq
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6
bioinformatics pipelines
Reads2map
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6
WDL workflows to build genetic maps from sequencing reads
Mondrian
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6
Reproducible Workflows
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6
Reproducible Workflows, curated at the Fred Hutch
Iplugexample
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6
IPlug "Tale" Edition example (tremolo effect).
Cellprofiler On Terra
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6
Run CellProfiler on Terra. Contains workflows that enable a full end-to-end Cell Painting pipeline.
Regenie Pipelines
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6
WDL pipelines for running regenie
Wgsincancerdiagnostics
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6
Analysis Wdls
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5
Scalable genomic analysis pipelines, written in WDL
Seaseq
⭐
5
Abraham's lab - ChipSeq Pipeline
Kccafeteria
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5
Project for 5th Semester Subject -> WDL & DBMS
Swipe
⭐
5
SFN-WDL infrastructure for pipeline execution - a template repository and Terraform module for SFN-WDL based projects
Fungal Wdl
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5
Broad fungal method repository
Bioinfo Praticas
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5
Prática para experimentar algumas ferramentas de desenvolvimento, no contexto de bioinfo.
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