Updating yml for formats

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

diff --git a/WGS-processing/cwl/helper/gather-vcf.cwl b/WGS-processing/cwl/helper/gather-vcf.cwl
index 15b6551f03d58fed449693976be9e2ba6cdbe654..4f796691af6d65db4349e9c954fa1aaa7600dba0 100644 (file)
--- a/WGS-processing/cwl/helper/gather-vcf.cwl
+++ b/WGS-processing/cwl/helper/gather-vcf.cwl
@@ -2,10 +2,6 @@ cwlVersion: v1.1
 class: CommandLineTool
 label: Gather GVCF using Picard 
 
-$namespaces:
-  arv: "http://arvados.org/cwl#"
-  cwltool: "http://commonwl.org/cwltool#"
-
 requirements:
   DockerRequirement:
     dockerPull: broadinstitute/gatk:4.1.7.0
@@ -15,16 +11,16 @@ requirements:
 hints:
   ResourceRequirement:
     ramMin: 20000
-    coresMin: 4    
+    coresMin: 4 
   arv:RuntimeConstraints:
     outputDirType: keep_output_dir
 
 inputs:
-  gvcfdir: 
+  gvcfdir:
     type: Directory
     label: Input directory of GVCFs
     loadListing: 'shallow_listing'
-  sample: 
+  sample:
     type: string
     label: Sample Name
   reference:
@@ -43,7 +39,7 @@ outputs:
   gatheredgvcf:
     type: File
     format: edam:format_3016 # GVCF
-    label: Gathered GVCF 
+    label: Gathered GVCF
     secondaryFiles:
       - .tbi
     outputBinding:
@@ -53,10 +49,10 @@ baseCommand: /gatk/gatk
 
 arguments:
   - "--java-options"
-  - "-Xmx8G" 
+  - "-Xmx8G"
   - MergeVcfs
   - shellQuote: false
-    valueFrom: | 
+    valueFrom: |
      ${function compare(a, b) {
       var baseA = a.basename;
       var baseB = b.basename;
@@ -68,7 +64,7 @@ arguments:
       comparison = -1;
       }
       return comparison;
-      } 
+      }
 
       var samples = [];
       for (var i = 0; i < inputs.gvcfdir.listing.length; i++) {
@@ -99,6 +95,6 @@ $namespaces:
  arv: "http://arvados.org/cwl#"
  cwltool: "http://commonwl.org/cwltool#"
 
-$schemas:
- - https://schema.org/version/latest/schema.rdf
- - http://edamontology.org/EDAM_1.18.owl
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl