From 86396f63fa01b893ebb174c27929f3d791846440 Mon Sep 17 00:00:00 2001 From: Sarah Wait Zaranek Date: Thu, 18 Jun 2020 00:59:37 +0000 Subject: [PATCH] removing un-needed yml Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek no issue # --- WGS-processing/README | 12 ++++++------ WGS-processing/yml/check-sam.yml | 7 ------- WGS-processing/yml/gather-vcf2.yml | 13 ------------- 3 files changed, 6 insertions(+), 26 deletions(-) delete mode 100644 WGS-processing/yml/check-sam.yml delete mode 100644 WGS-processing/yml/gather-vcf2.yml diff --git a/WGS-processing/README b/WGS-processing/README index 5b4b9b9..507fb3a 100644 --- a/WGS-processing/README +++ b/WGS-processing/README @@ -7,6 +7,12 @@ This directory contains an Arvados demo showing processing of whole genome seque Workflows are written in CWL v1.1. +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 + To run the workflow: 1. cd into cwl directory @@ -14,11 +20,5 @@ To run the workflow: 2. run the following: arvados-cwl-runner --no-wait --project-uuid YOUR_PROJECT_UUID wgs-processing-wf.cwl ../yml/YOURINPUTS.yml -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 - 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/). diff --git a/WGS-processing/yml/check-sam.yml b/WGS-processing/yml/check-sam.yml deleted file mode 100644 index e87a841..0000000 --- a/WGS-processing/yml/check-sam.yml +++ /dev/null @@ -1,7 +0,0 @@ -sam: - class: File - location: keep:147b9da57ceb51de9d653e870d8c019a+712/hu297A5D_AE2CH6SK4DG.bam - -reference: - class: File - location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa diff --git a/WGS-processing/yml/gather-vcf2.yml b/WGS-processing/yml/gather-vcf2.yml deleted file mode 100644 index 5f4e324..0000000 --- a/WGS-processing/yml/gather-vcf2.yml +++ /dev/null @@ -1,13 +0,0 @@ -reference: - class: File - location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa -sample: ERR1726424 -gvcf1: - class: File - location: keep:dec5da8ebcda12b3eece8705a4391f55+2510/ERR1726424.gatk.g.vcf.gz - -gvcf2: - class: File - location: keep:054cb90cfb20dedb862af1fdd636ad3f+297/ERR1726424_10.gatk.g.vcf.gz - - -- 2.30.2