Updating readme

Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

diff --git a/WGS-processing/README.md b/WGS-processing/README.md
index 4114f95567071e921713f6cb9440733c07177267..aa2d8e687cab773cca3f921d77fce9720198f6aa 100644 (file)
--- a/WGS-processing/README.md
+++ b/WGS-processing/README.md
@@ -1,9 +1,9 @@
 This directory contains an 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 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. 
 


@@ -16,9 +16,9 @@ Subdirectories are:
 To run the workflow:
 
 * cd into cwl directory
 To run the workflow:
 
 * cd into cwl directory

-
-* run the following
+* run the following:

   arvados-cwl-runner --no-wait --project-uuid YOUR_PROJECT_UUID wgs-processing-wf.cwl ../yml/YOURINPUTS.yml
 
 About the Demo Data:
   arvados-cwl-runner --no-wait --project-uuid YOUR_PROJECT_UUID 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/).