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analysis-wdls

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

arvados

an open source platform for managing and analyzing biomedical big data

bfx-workshop

cancer-genomics-workflow

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

civic-client

Web client for CIViC: Clinical Interpretations of Variants in Cancer

civic-docs

Source code for the civicdb.org docs

civic-server

Backend Server for CIViC Project

civic-v2

CIViC version 2 server & client projects

civic_svi_course

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

cloud-automation

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

cloud-workflows

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

cromwell

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

cromwell-deployment

Scripts and configuration to setup a Cromwell deployment

cwltool

Common Workflow Language reference implementation

docker-alignment_helper-cwl

docker-bam-readcount

Docker containerization for "bam-readcount"

docker-bcftools

Docker container for bcftools

docker-bcftools-cwl

Variant of bcftools image without an ENTRYPOINT

docker-bisulfite

a fat pipeline for running WGBS analysis

docker-checkstrandedness

docker-cle

Docker containerization for the CLE

docker-expansionhunter

Docker image for running https://github.com/Illumina/ExpansionHunter

docker-fp_filter-cwl

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

docker-fpfilter

Docker container for false positive filter

docker-fpfilter-cwl

version of docker-fpfilter without an entrypoint

docker-mapq0-filter

filter a vcf for variants with high percentage of mapq0 reads

docker-rnaseq

A fat docker image for running RnaSeq

docker-samtools

Docker container for Samtools

docker-samtools-cwl

docker-strelka

A docker image for Strelka