X-Git-Url: https://git.arvados.org/arvados-tutorial.git/blobdiff_plain/10ba8ab79262d0109f03d46c32d6898227c674c5..e3b01c795c65bbfa0c09f9e7b8ffb80a950746d7:/WGS-processing/README.md

diff --git a/WGS-processing/README.md b/WGS-processing/README.md
index 51a0551..dd38513 100644
--- a/WGS-processing/README.md
+++ b/WGS-processing/README.md
@@ -1,24 +1,27 @@
 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 an HTML report comparing variants against ClinVar archive 
+* Check of fastq quality using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) 
+* Local alignment using BWA-MEM (http://bio-bwa.sourceforge.net/bwa.shtml)
+* Variant calling in parallel using GATK Haplotype Caller (https://gatk.broadinstitute.org/hc/en-us)
+* Generation of an HTML report comparing variants against ClinVar archive (https://www.ncbi.nlm.nih.gov/clinvar/)
 
-Workflows are written in CWL v1.1. 
+Workflows are written in CWL v1.1. (https://www.commonwl.org/)
 
 Subdirectories are:
 * cwl - contains CWL code for the demo
-* yml - contains yml inputs for cwl demo code
+* 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 
 
 To run the workflow:
 
-* cd into cwl directory
-
-* run the following
-** arvados-cwl-runner --no-wait --project-uuid YOUR_PROJECT_UUID wgs-processing-wf.cwl ../yml/YOURINPUTS.yml
+*  arvados-cwl-runner --no-wait --project-uuid YOUR_PROJECT_UUID ./cwl/wgs-processing-wf.cwl ./yml/YOURINPUTS.yml
 
 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/). 
+
+WGS Data used in this demo is public data made available by the Personal Genome Project.  
+This set of data is from the PGP-UK (https://www.personalgenomes.org.uk/). 
+
+Have questions about Arvados?
+* https://arvados.org/
+* https://gitter.im/arvados/community