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 8a92726272133c31fd75e54cf977830d127584aa..424189e6405ff43e828d93fc4537feadba925523 100644 (file)
--- 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 d22173ff6c760014aa8d88cc6c48518e29ab0c3f..e813417d4ea1143876db4e8b877a9e3c121c4761 100644 (file)
--- 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 22a9af5d9f85b827bbd3db9024f21207e831f515..acff1edceab7cb06b9e17f7cb37bfa16503f8dfb 100644 (file)
--- 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 20b5a3b916449050ff08d56180db0b316a2b6b39..bf0b9899ef04f89501df4b5c41f279b95f8150b2 100644 (file)
--- 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