v2.0.1

There are numerous changes and updates in this release. GPU processing has been streamlined for WGS samples, there is now full WES support, and there are a host of wrapper scripts and utility resources to be used. This pipeline is the equivalent of BWA-MEM 0.7.15 and GATK 4.2 and uses NVIDIA's Clara Parabricks 4.0.0-1 and runs on WUSTL's HPC compute1 with LSF job management.

Full Changelog: v2.0...v2.0.1

WGS Sample and Joint Pipelines for Compute1

Overview

This release contains pipeline scripts for processing raw WGS data from input through to gVCF. The code is written specifically for the compute1 cluster at Washington University in St. Louis; however, most of the code only assumes an LSF job submission system, so the code should either be usable on other clusters with some modifications or directly usable on another LSF system. Additionally, the docker container code does not assume the same job submission system and may be more directly usable.

Organization

There are pipeline scripts for clusters and servers, wrapper scripts, and code for generating docker images in this release.

• Both the sample-level and cohort-level pipeline scripts for processing data on compute1 are in the base directory.
• Wrapper scripts to run components of the pipeline can be found in the wrapper directory.
• Code for generating the docker scripts are in the docker directory. The subfolders are named for the docker container they create. Scripts and data are often found in the /scripts directory within each docker's directory.
• The scripts in the Hydra directory are for use on servers.

WXS RG, SM, and Joint pipelines

WXS initial release that has made it to a full GitHub release. Naming is set to match image tags with associated existing docker images.

Running Pipelines

Each pipeline can be called from the the /scripts directory in the docker image. The other scripts are wrapper scripts for running the pipelines on compute1.