Updating cwl and yml for intervals and other changes

[arvados-tutorial.git] / WGS-processing / yml / wgs-processing-wf.yml

diff --git a/WGS-processing/yml/wgs-processing-wf.yml b/WGS-processing/yml/wgs-processing-wf.yml
index 8853a804a7ad036f404a7660b40589eaf0fc2fcf..299a674eaa08056538c86d0745dabd6e80dea04f 100644 (file)
--- a/WGS-processing/yml/wgs-processing-wf.yml
+++ b/WGS-processing/yml/wgs-processing-wf.yml
@@ -1,8 +1,11 @@
-sample: ERR1726424
-
 reference:
   class: File
-  location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
+  format: edam:format_1929
+  location: keep:5eac1d1c03ff6404226421a8d8351cf1+6133/GRCh38_no_alt_plus_hs38d1_analysis_set.fna 
+
+fullintervallist:
+  class: File
+  location: /data-sdd/pgp/testdata/full-noalt-scattered.interval_list
 
 fastqdir:
   class: Directory
@@ -10,6 +13,7 @@ fastqdir:
 
 clinvarvcf:
   class: File
+  format: edam:format_3016
   location: keep:242ba3b9049aee86ab2c72db4f3b2822+223/38/clinvar.vcf.gz
 
 reportfunc:
@@ -18,14 +22,17 @@ reportfunc:
 
 headhtml:
   class: File
+  format: edam:format_2331
   location: ../src/annotation/head.html
 
 tailhtml:
   class: File
+  format: edam:format_2331
   location: ../src/annotation/tail.html
 
-scattercount: '32'
+scattercount: '20'
 
 knownsites:
   class: File
+  format: edam:format_3016
   location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz