Updating readme and reorganization

[arvados-tutorial.git] / WGS-processing / README

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-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/).