X-Git-Url: https://git.arvados.org/arvados-tutorial.git/blobdiff_plain/3ee1659130fc7acdee08cf75aaeaba6528b56e72..b50ffeeeae865d0780ca03c5a3f5065eeeb758e4:/WGS-processing/cwl/helper/mark-duplicates.cwl

diff --git a/WGS-processing/cwl/helper/mark-duplicates.cwl b/WGS-processing/cwl/helper/mark-duplicates.cwl
index 3d7cba6..6041221 100644
--- a/WGS-processing/cwl/helper/mark-duplicates.cwl
+++ b/WGS-processing/cwl/helper/mark-duplicates.cwl
@@ -1,9 +1,6 @@
 cwlVersion: v1.1
 class: CommandLineTool
-label: Marking Duplicates using Picard 
-$namespaces:
-  arv: "http://arvados.org/cwl#"
-  cwltool: "http://commonwl.org/cwltool#"
+label: Marking Duplicates using GATK (Picard) 
 
 requirements:
   DockerRequirement:
@@ -15,18 +12,28 @@ hints:
     coresMin: 4    
   arv:RuntimeConstraints:
     outputDirType: keep_output_dir
+  SoftwareRequirement:
+    packages:
+      GATK:
+        specs: [ "https://identifiers.org/rrid/RRID:SCR_001876" ]
+        version: [ "4.1.7" ]
 
 inputs:
   bam:
     type: File
+    format: edam:format_2572 # BAM
+    label: Sorted BAM 
 
 outputs:
   dupbam:
     type: File
+    format: edam:format_2572 # BAM
+    label: Sorted BAM with labeled duplicates
     outputBinding:
       glob: "*.bam"
   dupmetrics:
     type: File
+    label: Duplication metrics file
     outputBinding:
       glob: "*.txt"
 
@@ -41,4 +48,17 @@ arguments:
   - prefix: "-O"
     valueFrom: marked_dups$(inputs.bam.basename)
   - prefix: "-M"
-    valueFrom: "metrics.txt" 
+    valueFrom: "metrics.txt"
+
+s:codeRepository: https://github.com/arvados/arvados-tutorial
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+ arv: "http://arvados.org/cwl#"
+ cwltool: "http://commonwl.org/cwltool#"
+
+$schemas:
+ - https://schema.org/version/latest/schema.rdf
+ - http://edamontology.org/EDAM_1.18.owl