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

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

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

An example implementation for the Cromwell workflow management system on PBS Pro

Example Repository for setting up GitHub Actions for WDL and CWL workflows for CI/CD

Automated and reproducible tool for identifying genomic variants at scale ☕️

Focused on constructing a phylogenetic tree from Philippine strains of Candida albicans.

Automation tool for high-throughput sequencing DNA methylation data

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

Cromwell pipelines for human genetic data

varscan repo contains code for Varscan workflow

Workflow pipelines for the Solita TRE