{"repo":"NCI-GDC/gdc-workflow-overview","free":true,"listed":false,"github":"https://github.com/NCI-GDC/gdc-workflow-overview","clone":"git clone https://github.com/NCI-GDC/gdc-workflow-overview.git","description":"Overview of GDC Harmonization Workflows","language":null,"stars":43,"topics":["bioinformatics","workflow","overview"],"license":"Apache-2.0","category":"workflow-automation","readme_excerpt":"Overview of GDC Harmonization Workflows Description - Here are the overview of major GDC harmonization workflows. - The GDC workflow repositories has been tested on GDC data and in the particular environment GDC is running in. - Current GDC production workflows are running in the GDC Pipeline Automation System (GPAS). - Most GDC workflows are developed using Common Workflow Language (CWL) with Dockerized tools. - Please check GDC Documentation for more details. For external users The GDC workflow repositories has been tested on GDC data and in the particular environment GDC is running in. - We have created external CWL entrypoint in some workflows. For the others, you are expecting to modify the workflow to be used in your system. - Some of the reference data required for the workflow production are hosted in GDC reference files. We can not share some other reference files due to licensing issues. - In particular, we can not share target or bait bed files or interval list of any specific Target Capture Kits. You are encouraged to contact the vendors or project owners to get these files. - We are not able to share dockers to external users due to licensing issues. You are welcomed to build your own dockers using the docker files provided. - For any questions related to GDC data, please contact the GDC Help Desk at support@nci-gdc.datacommons.io. Production Workflows Include DNA-Seq Alignment - BWA based alignment workflow for Whole Exome Sequencing (WXS), Whole Genome Sequenci","default_branch":null,"files":null,"tree":[],"storefront":"/r/NCI-GDC","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/NCI-GDC/gdc-workflow-overview/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}