wdl-workflow

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

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.

Rust crates for working with Workflow Description Language (WDL) documents.

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

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

Create WDL documentation using Markdown.

[Experimental] Workflow Definition Language (WDL) to CWL

A command-line tool for executing, managing, and querying WDL workflows on Cromwell servers.

WDL pipelines for the Sentieon tools

Broad fungal method repository

Visual Studio Code extension for Sprocket.

Run Sprocket as part of a CI/CD pipeline with GitHub Actions.

Pipeline to characterize Human Endogenous Retrovirus (HERV) expression

WDL tasks for commonly used BFX tools

Illustrative examples using WDL best practices.

Workflow for metagenome assembly

A pipeline for mitochondrial mutation calling

A cloud-based pipeline to estimate telomere lengths from WGS data using Telseq

This tool provides a modular WDL-Docker-Cromwell environment for rMAP, a bioinformatics pipeline for analyzing microbial genomic data, genome assembly & profiling of the resistome, mobilome & virulome, as well as pangenome & MLST typing, BLASTn & phylogenetic analysis. It includes all required tools, enabling reproducible & scalable analysis

A robust, Dockerized WDL/Cromwell workflow for Mycobacterium tuberculosis complex genomic surveillance, integrating read trimming, QC, species typing, TB-Profiler resistance & lineage profiling, NTM/MTBC identification, mutation evidence reporting, core-SNP phylogenomics, SNP distance analysis & interactive HTML reporting for TB AMR surveillance.