updating yml

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

diff --git a/yml/bwa-gatk-report-wf-UK.yml b/yml/bwa-gatk-report-wf-UK.yml
index 1dfba1679dd7b4a826c90f27d9a531eb6132ed0d..074d16a2aa0600825499d5047b729a1a4a196afe 100644 (file)
--- a/yml/bwa-gatk-report-wf-UK.yml
+++ b/yml/bwa-gatk-report-wf-UK.yml
@@ -27,3 +27,9 @@ headhtml:
 tailhtml:
   class: File
   location: /data-sdd/pgp/arvados-tutorial/src/annotation/tail.html
+
+scattercount: '32'
+
+knownsites:
+  class: File
+  location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz

diff --git a/yml/gather-vcf.yml b/yml/gather-vcf.yml
index 779a97c2fba031d215f76c66f4ed10a8ddcc3e06..ca2a0519ac5096bffca254f5599687b259bc6c71 100644 (file)
--- a/yml/gather-vcf.yml
+++ b/yml/gather-vcf.yml
@@ -2,16 +2,7 @@ reference:
   class: File
   location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
 sample: ERR1726424
-gvcflist:
-  class: File
-  location: /data-sdd/pgp/arvados-tutorial/src/variantcalling/sample-files.list
-gvcf1:
-  class: File
-  location: keep:dec5da8ebcda12b3eece8705a4391f55+2510/ERR1726424.gatk.g.vcf.gz
-
-gvcf2:
-  class: File
-  location: keep:dec5da8ebcda12b3eece8705a4391f55+2510/ERR1726424.gatk.g.vcf_10.gz
-
-
+gvcfdir:
+  class: Directory
+  location: keep:1da945b644da2182d010fb1b7745233f+2725
 

diff --git a/yml/getgvcfs.yml b/yml/getgvcfs.yml
new file mode 100644 (file)
index 0000000..1c646ee
--- /dev/null
+++ b/yml/getgvcfs.yml
@@ -0,0 +1,3 @@
+gvcfdir:
+  class: Directory 
+  location: keep:1da945b644da2182d010fb1b7745233f+2725