From: Sarah Wait Zaranek Date: Fri, 19 Jun 2020 21:07:50 +0000 (+0000) Subject: Updating readme X-Git-Url: https://git.arvados.org/arvados-tutorial.git/commitdiff_plain/440359f6c68cd22ac664ccacda5a71a393985c43 Updating readme Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek no issue # --- diff --git a/WGS-processing/README.md b/WGS-processing/README.md index 4114f95..aa2d8e6 100644 --- 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: -* 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. @@ -16,9 +16,9 @@ Subdirectories are: 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: -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/).