A companion for the Cromwell Server

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

Web-based interface to the NMDC EDGE platform

varscan repo contains code for Varscan workflow

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

Create WDL documentation using Markdown.

Genomic data processing pipelines written in WDL making use of Docker containers to ensure stability.

A WDL-based workflow for profiling Klebsiella & E. coli genomes using Kleborate. Supports local execution with Cromwell both local & cloud deployment in Terra, enabling automated analysis of assemblies with docker & integration with Terra data tables for scalable genomic surveillance.

A free, legal BIOS replacement for the original Xbox

Rich IDE support for Workflow Description Language

Robust Eukaryotic Annotation Toolkit

Configure workflow/pipeline tests using yaml files.

CLI for interacting with Cromwell servers

ACES is a workflow to query small sequences in a large set of genomes. It provides several outputs including BLAST results, a multiple sequence alignment file, a graphical fragment assembly file, and a phylogenetic tree file.

Client for the Cromwell workflow engine

A repo containing instructions for running a Cromwell server on Gizmo at the Fred Hutch. (Contact Amy Paguirigan for questions)

Dashboard for better visual at workflows on Cromwell server

Automated and reproducible tool for identifying genomic variants at scale ☕️

A CGI for getting the status of a workflow execution in Cromwell

An integrated analysis platform for efficiently achieving computational reproducibility