WGS-processing/README.md

   1 This directory contains an Arvados demo showing processing of whole genome sequencing (WGS) data. The workflow includes:
   2
   3 * Check of fastq quality using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
   4 * Local alignment using BWA-MEM (http://bio-bwa.sourceforge.net/bwa.shtml)
   5 * Variant calling in parallel using GATK Haplotype Caller (https://gatk.broadinstitute.org/hc/en-us)
   6 * Generation of an HTML report comparing variants against ClinVar archive (https://www.ncbi.nlm.nih.gov/clinvar/)
   7
   8 Workflows are written in CWL v1.1. (https://www.commonwl.org/)
   9
  10 Subdirectories are:
  11 * cwl - contains CWL code for the demo
  12 * yml - contains YML inputs for cwl demo code
  13 * src - contains any src code for the demo
  14 * docker - contains dockerfiles necessary to re-create any needed docker images
  15
  16 To run the workflow:
  17
  18 *  arvados-cwl-runner --no-wait --project-uuid YOUR_PROJECT_UUID ./cwl/wgs-processing-wf.cwl ./yml/YOURINPUTS.yml
  19
  20 About the Demo Data:
  21
  22 WGS Data used in this demo is public data made available by the Personal Genome Project.
  23 This set of data is from the PGP-UK (https://www.personalgenomes.org.uk/).
  24
  25 Have questions about Arvados?
  26 * https://arvados.org/
  27 * https://gitter.im/arvados/community
  28
  29 Have questions about CWL?
  30 * https://www.commonwl.org/
  31 * https://cwl.discourse.group/
  32 * https://gitter.im/common-workflow-language/common-workflow-language