Adding links about CWL to the readme

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

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 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
-src - contains any src code for the demo
-docker - contains dockerfiles necessary to re-create any needed docker images 
+* 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 
 
 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
+*  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
+
+Have questions about CWL?
+* https://www.commonwl.org/
+* https://cwl.discourse.group/
+* https://gitter.im/common-workflow-language/common-workflow-language