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 cd1532c7deb91bcc6d6b5e7fd69a9f512f64484c..4f796691af6d65db4349e9c954fa1aaa7600dba0 100644 (file)
--- a/WGS-processing/cwl/helper/gather-vcf.cwl
+++ b/WGS-processing/cwl/helper/gather-vcf.cwl
@@ -1,9 +1,6 @@
 cwlVersion: v1.1
 class: CommandLineTool
-label: Gathering vcf using Picard 
-$namespaces:
-  arv: "http://arvados.org/cwl#"
-  cwltool: "http://commonwl.org/cwltool#"
+label: Gather GVCF using Picard 
 
 requirements:
   DockerRequirement:
@@ -14,18 +11,22 @@ 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
+    label: Input directory of GVCFs
     loadListing: 'shallow_listing'
-  sample: string
+  sample:
+    type: string
+    label: Sample Name
   reference:
     type: File
+    format: edam:format_1929 # FASTA
+    label: Reference genome
     secondaryFiles:
       - .amb
       - .ann
@@ -37,6 +38,8 @@ inputs:
 outputs:
   gatheredgvcf:
     type: File
+    format: edam:format_3016 # GVCF
+    label: Gathered GVCF
     secondaryFiles:
       - .tbi
     outputBinding:
@@ -46,10 +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;
@@ -61,7 +64,7 @@ arguments:
       comparison = -1;
       }
       return comparison;
-      } 
+      }
 
       var samples = [];
       for (var i = 0; i < inputs.gvcfdir.listing.length; i++) {
@@ -82,3 +85,16 @@ 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