-Arvados demo showing processing of whole genome sequencing (WGS) data. The workflow includes:
+This directory contains an Arvados demo showing processing of whole genome sequencing (WGS) data. The workflow includes:
+* Check of fastq quality
* Local alignment using BWA-MEM
* Variant calling in parallel using GATK
-* Generation of HTML Report showing Comparision of Variants with ClinVar Public Archive
+* Generation of an HTML report comparing variants against ClinVar archive
-Workflows are written in CWL
+Workflows are written in CWL v1.1.
+
+To run the workflow:
+
+1. cd into cwl directory
+
+2. run the following:
+arvados-cwl-runner --no-wait --project-uuid YOUR_PROJECT_UUID wgs-processing-wf.cwl ../yml/YOURINPUTS.yml
+
+Subdirectories are:
+cwl - contains CWL code for the demo
+yml - contains yml inputs for cwl demo code
+src - contains any src code for the demo
+docker - contains dockerfiles necessary to re-create any needed docker images
+
+About the Demo Data:
+WGS Data used in this demo is public data made available by the Personal Genome Project. This data is from the PGP-UK (https://www.personalgenomes.org.uk/).