https://github.com/stjudecloud/workflows

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

bioinformatics bioinformatics-workflows computational-biology cromwell cwl cwl-workflow genomics next-generation-sequencing stjudecloud wdl wdl-workflow workflow workflow-engine workflows

Last synced: 19 Feb 2026

https://github.com/stjudecloud/wdldoc

Create WDL documentation using Markdown.

bioinformatics computational-biology cromwell genomics next-generation-sequencing stjudecloud wdl wdl-workflow workflow

Last synced: 13 Apr 2025

https://github.com/stjudecloud/ngsderive

Forensic analysis tool useful in backwards computing information from next-generation sequencing data.

bioinformatics computational-biology gene-model genomics next-generation-sequencing ngs strandedness strandedness-inference workflow workflow-engine

Last synced: 11 Jul 2025

https://github.com/stjudecloud/university

Educational materials for the St. Jude Cloud project.

Last synced: 11 Jul 2025

https://github.com/stjudecloud/ecc

The Encyclopedia of Composable Characteristics (ECC).

Last synced: 16 Mar 2026

https://github.com/stjudecloud/expression-classification

Last synced: 26 Jul 2025

https://github.com/stjudecloud/mtsg

Find and quantify COSMIC mutational signatures across samples

Last synced: 29 Jul 2025

https://github.com/stjudecloud/bioinformatics-tool-template

Last synced: 19 Mar 2026

https://github.com/stjudecloud/merge-counts

Utility for merging RNA-seq expression counts files from St. Jude Cloud.

Last synced: 11 Jul 2025

https://github.com/stjudecloud/cloud-app-tutorial

Cloud application examples for St. Jude Cloud.

cloud documentation genomics stjudecloud tutorial workflow workflow-engine

Last synced: 11 Feb 2026

https://github.com/stjudecloud/rfcs

Request for Comments (RFCs) on the St. Jude Cloud Project.

bioinformatics bioinformatics-pipeline computational-biology cwl cwl-workflow discussion genomics proposal rfcs stjudecloud wdl wdl-workflow workflow workflow-engine

Last synced: 15 Feb 2026

https://github.com/stjudecloud/theme

Component library and CSS themes for applications on the St. Jude Cloud project.

bootstrap css fonts react sass stjudecloud tailwindcss theme vue

Last synced: 24 Oct 2025

https://github.com/stjudecloud/docs

Educational materials for the St. Jude Cloud project.

Last synced: 26 Jan 2026

https://github.com/stjudecloud/release-python-action

Github Action to release a Poetry-based Python app as we regularly do on the St. Jude Cloud project.

Last synced: 07 Feb 2026

https://github.com/stjudecloud/cgc-go

Last synced: 27 Feb 2026

https://github.com/stjudecloud/dx-rapid_rnaseq

Last synced: 16 Feb 2026

https://github.com/stjudecloud/dx-star

DNAnexus app wrapper for STAR alignment

Last synced: 12 Jul 2025

https://github.com/stjudecloud/utilities

Utility scripts created for and used on the St. Jude Cloud team.

Last synced: 03 Jul 2026

https://github.com/stjudecloud/dx-rnaseq_standard

Monolithic DNAnexus implementation of RNA-Seq V2 pipeline with miniwdl

Last synced: 26 Jul 2025

https://github.com/stjudecloud/stjude_htseq_count

Last synced: 25 Aug 2025

https://github.com/stjudecloud/msgenctl

CLI to manage Microsoft Genomics workflows

Last synced: 15 Mar 2025

https://github.com/stjudecloud/dx-tag_outputs

Last synced: 22 Jul 2025

https://github.com/stjudecloud/dx-fuzzion

DNAnexus implementation of Fuzzion (https://github.com/stjude/fuzzion)

Last synced: 15 Mar 2025

https://github.com/stjudecloud/cde-transformers

TODO

Last synced: 15 Mar 2025

https://github.com/stjudecloud/dx-manta

Last synced: 15 Mar 2025

https://github.com/stjudecloud/dx-build_visualizer

Last synced: 09 Jul 2025

https://github.com/stjudecloud/dx-coverage_bw

Last synced: 15 Mar 2025