Bioinformatics workflows developed for and used on the St. Jude Cloud project.
WDL pipelines for the Sentieon tools
Broad fungal method repository
WDL tasks for commonly used BFX tools
Workflow for metagenome assembly
A cloud-based pipeline to estimate telomere lengths from WGS data using Telseq
This is the repository for the WDL and JSON files accompanying the WDL 101 course.
Variant Calling and Annotation using PacBio Hi-Fi Reads
A collection of tasks wrapped in WDL
A repo containing workflows written in WDL to test using the Fred Hutch Cromwell configuration.
A workflow for processing metagenomics data sets using Centrifuge. Category:Single-Sample
RNA binding workflow geared towards broad discovery of binding sites
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
Strelka2 somatic variant calling workflow
Bioinformatics workflows developed for and used on the St. Jude Cloud project.
Workflow Description Language (WDL) test workflow. Write custom messages as file outputs. For testing Cloud WS APIs and the GA4GH Starter Kit.
Workflow Description Language (WDL) test workflow. Write hardcoded messages to stdout. For testing Cloud WS APIs and the GA4GH Starter Kit.
Variant calling WDL workflow using a trio of variant callers and analyzing consensus among them
Focused on constructing a phylogenetic tree from Philippine strains of Candida albicans.
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