Bugfix .bai secondary file for ApplyBSQR behavior

[arvados-tutorial.git] / WGS-processing / cwl / helper / gather-array-vcf.cwl

diff --git a/WGS-processing/cwl/helper/gather-array-vcf.cwl b/WGS-processing/cwl/helper/gather-array-vcf.cwl
index 9daf557c48c592a39832991551c5a383d7a2bfbf..1e7d705bb7febf77436143eb089ebfa9c3aede6f 100644 (file)
--- a/WGS-processing/cwl/helper/gather-array-vcf.cwl
+++ b/WGS-processing/cwl/helper/gather-array-vcf.cwl
@@ -1,9 +1,6 @@
 cwlVersion: v1.1
 class: CommandLineTool
 label: Gather GVCFs
-$namespaces:
-  arv: "http://arvados.org/cwl#"
-  cwltool: "http://commonwl.org/cwltool#"
 
 requirements:
   DockerRequirement:
@@ -21,9 +18,15 @@ hints:
 inputs:
   gvcfarray: 
     type: File[] 
-  sample: string
+    format: edam:format_3016 # GVCF
+    label: GVCFs for given intervals
+  sample: 
+    type: string
+    label: Sample Name
   reference:
     type: File
+    format: edam:format_1929 # FASTA
+    label: Reference genome
     secondaryFiles:
       - .amb
       - .ann
@@ -35,6 +38,8 @@ inputs:
 outputs:
   gatheredgvcf:
     type: File
+    format: edam:format_3016 # GVCF
+    label: Gathered GVC
     secondaryFiles:
       - .tbi
     outputBinding:
@@ -83,3 +88,16 @@ arguments:
       }
   - prefix: "-O"
     valueFrom: $(inputs.sample).g.vcf.gz
+
+s:codeRepository: https://github.com/arvados/arvados-tutorial
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+
+$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