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UC Santa Cruz Computational Genomics Lab's Toil-based RNA-seq pipeline
The UCSC Genomics Institute's Computational Genomics Platform (CGP). This repo contains the Docker compose-based deployment process.
Workflow for variant callers MuSE, MuTect, SomaticSniper, and Pindel
All code for reproducing reference graph bakeoff results
The BD2K Python module kitchen sink
Proxy in front of dcc services ensuring the right people are passed through with the right privileges
Modern Toil Workflows
a place for topmed workflows
Scripts and schemas for JSON documents used with the DCC storage system and for building Elasticsearch indexes
A place for our business logic written in Luigi that triggers workflow launches.
This is a playbook that sets up a container host which can run workflows in containers
A Dockstore tool designed to perform file downloads from Redwood, run another Dockstore tool, and then upload to Redwood.
Runs STARFusion and arriba
Implementation of structural variant finding algorithm arriba by Sebastian Uhrig
The submission system client that uploads data/metadata to Redwood and indicates to the Spinnaker web service that a submission bundle is ready for validation.
Issues representing platform epics, user stories, tasks, etc. that are not specific to an existing component repository.
Image and VM management for Jenkins, Spark and Mesos clusters in EC2
The repository for the Toil TOPMed alignment best practice workflow.
Toil workflows for common genomic pipelines
Cloud object-based storage system for ICGC data
Runs ADTEx and Varscan copynumber on input exome bam files
Varscan copynumber variation caller workflow
test repo for core operation
A common library for functions and tools used in toil-based pipelines
a place to track work on the GA4GH Dream Challenges
Most used topics