Updating cwl and yml for intervals and other changes

[arvados-tutorial.git] / WGS-processing / yml / helper / scatter-gatk-wf-with-interval.yml

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..20b5a3b916449050ff08d56180db0b316a2b6b39 100644 (file)
--- a/WGS-processing/yml/helper/scatter-gatk-wf-with-interval.yml
+++ b/WGS-processing/yml/helper/scatter-gatk-wf-with-interval.yml
@@ -1,15 +1,22 @@
 bam:
   class: File
+  format: edam:format_2572
   location: keep:377c02de508dff9e4474f9a48d754933+53821/marked_dupsERR1726424.sorted.bam 
 
 reference:
   class: File
+  format: edam:format_1929
   location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
 
+fullintervallist:
+  class: File
+  location: /data-sdd/pgp/testdata/full-noalt-scattered.interval_list
+
 sample: ERR1726424
 
 scattercount: '32'
 
-knownsites1:
+knownsites:
   class: File
+  format: edam:format_3016
   location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz