Infrastructure and tooling required to get genomic workflows running in the cloud

Workflow used for WGS data QC

Aggregate results from bioinformatics analyses across many samples into a single report.

A hands on course explaining how to complete somatic cancer variant interpretation using CIViC and current guidelines

Early stages of converting genome/analysis-workflows from CWL to WDL

OTTR: Open-source Tools for Training Resources. This is template repository for creating online courses to be published on multiple platforms. See here: https://jhudatascience.org/OTTR_Template/ fo…

For report checks for OTTR Github Actions.

Pilot test for using the Arvados system to create new MGI cancer pipelines.

A scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python

Docker container for Samtools

STAR-Fusion codebase

filter a vcf for variants with high percentage of mapq0 reads

Tutorial to run immuno.wdl on Google Cloud

CIViC version 2 server & client projects

Given the output directory of a QC pipeline and a threshold config file, parse out the desired metrics and evalute them against the thresholds.

Load your GCS bucket inventory into BigQuery fast with this tool.

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

This is the one used in current CWL pipelines - pulls from fpfilter-tool

Automation for standing up Gen3 commons on AWS, GCP, Azure, and on-prem