1 This directory contains an Arvados demo showing processing of whole genome sequencing (WGS) data. The workflow includes:
3 * Check of fastq quality
4 * Local alignment using BWA-MEM
5 * Variant calling in parallel using GATK
6 * Generation of an HTML report comparing variants against ClinVar archive
8 Workflows are written in CWL v1.1.
12 1. cd into cwl directory
15 arvados-cwl-runner --no-wait --project-uuid YOUR_PROJECT_UUID wgs-processing-wf.cwl ../yml/YOURINPUTS.yml
18 cwl - contains CWL code for the demo
19 yml - contains yml inputs for cwl demo code
20 src - contains any src code for the demo
21 docker - contains dockerfiles necessary to re-create any needed docker images
24 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/).