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
projects / arvados-tutorial.git / blobdiff