Switching variable knownsites1 to knownsites in yml files

Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

diff --git a/WGS-processing/yml/helper/gatk-baserecalibrator-with-interval.yml b/WGS-processing/yml/helper/gatk-baserecalibrator-with-interval.yml
index 7e6b16a9696b70aa713f604c4b96bcbac81873c5..d22173ff6c760014aa8d88cc6c48518e29ab0c3f 100644 (file)
--- a/WGS-processing/yml/helper/gatk-baserecalibrator-with-interval.yml
+++ b/WGS-processing/yml/helper/gatk-baserecalibrator-with-interval.yml
@@ -8,7 +8,7 @@ reference:
 
 sample: ERR1726424
 
 
 sample: ERR1726424
 

-knownsites1:
+knownsites:

   class: File
   location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz
 
   class: File
   location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz
 

diff --git a/WGS-processing/yml/helper/gatk-wf-with-interval.yml b/WGS-processing/yml/helper/gatk-wf-with-interval.yml
index 5761d1d01fa8044fb18708f7d5dd8dffc021d64d..e1e2b942056cbd52b23e3bdca77937ddbcec3436 100644 (file)
--- a/WGS-processing/yml/helper/gatk-wf-with-interval.yml
+++ b/WGS-processing/yml/helper/gatk-wf-with-interval.yml
@@ -1,13 +1,17 @@
 bam:
   class: File
   location: keep:377c02de508dff9e4474f9a48d754933+53821/marked_dupsERR1726424.sorted.bam 
 bam:
   class: File
   location: keep:377c02de508dff9e4474f9a48d754933+53821/marked_dupsERR1726424.sorted.bam 

+

 reference:
   class: File
   location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
 reference:
   class: File
   location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa

+

 intervallist:
   class: File
   location: keep:4d4947f6637f0acec32580e09d991967+815/0000-scattered.interval_list
 intervallist:
   class: File
   location: keep:4d4947f6637f0acec32580e09d991967+815/0000-scattered.interval_list

+

 sample: ERR1726424
 sample: ERR1726424

-knownsites1:
+
+knownsites:

   class: File
   location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz
   class: File
   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 f6d49433fc0f88f263e1d51665c7732e7e3eb95d..4a36ecb8534c6a8534fae2cae47b98520c8a52bc 100644 (file)
--- a/WGS-processing/yml/helper/scatter-gatk-wf-with-interval.yml
+++ b/WGS-processing/yml/helper/scatter-gatk-wf-with-interval.yml
@@ -10,6 +10,6 @@ sample: ERR1726424
 
 scattercount: '32'
 
 
 scattercount: '32'
 

-knownsites1:
+knownsites:

   class: File
   location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz
   class: File
   location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz