From: Sarah Wait Zaranek <swz@curii.com>
Date: Mon, 27 Jul 2020 20:08:24 +0000 (+0000)
Subject: Updating yml for 2 vcfs of known sites
X-Git-Url: https://git.arvados.org/arvados-tutorial.git/commitdiff_plain/7521f8770b81d944aad3c1e0fd7ef5a886600190

Updating yml for 2 vcfs of known sites
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #
---

diff --git a/WGS-processing/yml/helper/bwamem-gatk-report-wf.yml b/WGS-processing/yml/helper/bwamem-gatk-report-wf.yml
index 8a92726..424189e 100644
--- a/WGS-processing/yml/helper/bwamem-gatk-report-wf.yml
+++ b/WGS-processing/yml/helper/bwamem-gatk-report-wf.yml
@@ -40,7 +40,12 @@ tailhtml:
 
 scattercount: '32'
 
-knownsites:
+knownsites1:
+  class: File
+  format: edam:format_3016
+  location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.dbsnp138.vcf
+
+knownsites2:
   class: File
   format: edam:format_3016
   location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz
diff --git a/WGS-processing/yml/helper/gatk-baserecalibrator-with-interval.yml b/WGS-processing/yml/helper/gatk-baserecalibrator-with-interval.yml
index d22173f..e813417 100644
--- a/WGS-processing/yml/helper/gatk-baserecalibrator-with-interval.yml
+++ b/WGS-processing/yml/helper/gatk-baserecalibrator-with-interval.yml
@@ -8,8 +8,14 @@ reference:
 
 sample: ERR1726424
 
-knownsites:
+knownsites1:
   class: File
+  format: edam:format_3016
+  location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.dbsnp138.vcf
+
+knownsites2:
+  class: File
+  format: edam:format_3016
   location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz
 
 intervallist:
diff --git a/WGS-processing/yml/helper/gatk-wf-with-interval.yml b/WGS-processing/yml/helper/gatk-wf-with-interval.yml
index 22a9af5..acff1ed 100644
--- a/WGS-processing/yml/helper/gatk-wf-with-interval.yml
+++ b/WGS-processing/yml/helper/gatk-wf-with-interval.yml
@@ -14,7 +14,12 @@ intervallist:
 
 sample: ERR1726424
 
-knownsites:
+knownsites1:
+  class: File
+  format: edam:format_3016
+  location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.dbsnp138.vcf
+
+knownsites2:
   class: File
   format: edam:format_3016
   location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz
diff --git a/WGS-processing/yml/helper/scatter-gatk-wf-with-interval.yml b/WGS-processing/yml/helper/scatter-gatk-wf-with-interval.yml
index 20b5a3b..bf0b989 100644
--- a/WGS-processing/yml/helper/scatter-gatk-wf-with-interval.yml
+++ b/WGS-processing/yml/helper/scatter-gatk-wf-with-interval.yml
@@ -16,7 +16,12 @@ sample: ERR1726424
 
 scattercount: '32'
 
-knownsites:
+knownsites1:
+  class: File
+  format: edam:format_3016
+  location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.dbsnp138.vcf
+
+knownsites2:
   class: File
   format: edam:format_3016
   location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz