Top 31 wdl open source projects

DSDE Deep Learning Club

Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools

A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample

Repository for the Broad Institute Proteogenomic Data Analysis Center (PGDAC) established by the NIH Clinical Proteomics Tumor Analysis Consortium (CPTAC)

WDL plugin for pytest

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

A structural variation pipeline for short-read sequencing

WDL and CWL compiler for the DNAnexus platform

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

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

Single Cell Analysis Pipelines

Workflow Description Language - Specification and Implementations

Educational materials for learning WDL

Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://github.com/gatk-workflows/five-dollar-genome-analysis-pipeline

Portable WDL workflows for IDseq production pipelines

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.

Workflows for processing RNA data for germline short variant discovery with GATK (v3+v4) and related tools

Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.

Tutorials, workflows, and convenience scripts for Single Cell Portal

FusionInspector code

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

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 This Repository has been archived, please visit the link the ReadMe to obtain the latest version of the workflow.

Workflow Description Language compiler for the DNAnexus platform

Our VM/Docker sharing infrastructure and management component

bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.

Workflows for germline short variant discovery with GATK4

CLI for interacting with Cromwell servers

MOsaic CHromosomal Alterations (MoChA) caller

[Experimental] Workflow Definition Language (WDL) to CWL

minimal example implementations for bioinformatics workflow managers

A community menagarie of automated variant validations using bcbio and the Common Workflow Language