icgc-tcga-pancancer Goto Github PK

architecture-setup

This tool is used to install Bindle and its dependencies

awesome-wfpkgs1

awesome-wfpkgs2

broadwrapperworkflow

A SeqWare workflow that wraps the Broad workflow

bwa-decider

This repo is used for scheduling BWA workflows with architecture2 of the PanCancer Project

bwa-workflow

This is the workflow used by the PanCancer project for alignment

central-decider

This tool is intended to be used to scheduled VCF workflows for the PanCancer project. It reads from the centralized Elasticsearch database and keeps track of what has been scheduled in one central location.

central-decider-client

This tool is used to generate workflow.ini files from ini templates and information gather from the central-decider server.

ceph_transfer_ops

cgp-somatic-docker

Dockerised and simplified version of SeqWare-CGP-SomaticCore

cli

A common pancancer command line interface

container-host-bag

This is a playbook that sets up a container host which can run workflows in containers

demo-pkgs1

demo-pkgs2

demo-tool-pkgs

demo-wf-pkgs

demo-wfs

dewrapperworkflow

This is a workflow which aggregates the results of the EMBL and DKFZ workflows as one SeqWare workflow

dkfz_dockered_workflows

This is the container that houses the Roddy-based component provided by DKFZ for the DEWrapper workflow

ega-submission-tool

fastq-uploader

This tool is inteded to be used to upload fastq files for the PanCancer project

ga4gh-dream_workflow_execution_challenge

Repository for staging PCAWG workflows into GA4GH-DREAM Workflow Execution Challenge

gt-download-upload-wrapper

This tool is used to monitor and make gt-download more robust. To be use primarily withing SeqWare workflows

minibam-icgc-generator-jt

monitoring-bag

A playbook that sets up sensu client+ server and other tools such as logstash

mutationsigofsomaticsv

PCAWG mutation signatures analysis of somatic SVs

oxog-dockstore-tools

A CWL version of the Seqware OxoG workflow. This repository also contains scripts and dockerfiles used by the stand-alone versions of these components.

oxog-ops

Github repo for scheduling and tracking OxoG workflow jobs

oxog_varbam_annotate_wf_runner-jt

oxogwrapperworkflow

This workflow is a wrapper around the OxoG component.