Updating yml for formats

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

diff --git a/WGS-processing/cwl/helper/gvcf-to-vcf.cwl b/WGS-processing/cwl/helper/gvcf-to-vcf.cwl
index dfa3e248da1c19dcd5426cdee894dcd0e8d81f96..7df5fe2eee41a0b08dde333102eb61726603ab03 100644 (file)
--- a/WGS-processing/cwl/helper/gvcf-to-vcf.cwl
+++ b/WGS-processing/cwl/helper/gvcf-to-vcf.cwl
@@ -1,33 +1,45 @@
 cwlVersion: v1.1
 class: CommandLineTool
-label: Converts gvcf to vcf
+label: Convert GVCF to VCF
 
 requirements:
-  - class: DockerRequirement
+  DockerRequirement:
     dockerPull: curii/clinvar-report
-  - class: ShellCommandRequirement
+  ShellCommandRequirement: {}
 
 hints:
   ResourceRequirement:
     ramMin: 10000
     coresMin: 4
-
+  SoftwareRequirement:
+    packages:
+      BCFtools:
+        specs: [ "https://identifiers.org/rrid/RRID:SCR_005227" ]
+        version: [ "1.10.2" ]
+      HTSlib:
+        version: [ "1.10.2" ]
+        
 inputs:
-  samplename:
+  sample:
     type: string
+    label: Sample Name
   gvcf:
     type: File
+    format: edam:format_3016 # GVCF
+    label: GVCF generated from GATK
   
 outputs:
   vcf:
     type: File
+    format: edam:format_3016 # VCF
+    label: VCF extracted from GVCF
     outputBinding:
       glob: "*.vcf.gz"
     secondaryFiles: [.tbi]
 
 arguments:
   - bcftools
-  - view 
+  - view
   - prefix: "--min-ac"
     valueFrom: "1"
   - $(inputs.gvcf.path)
@@ -35,10 +47,21 @@ arguments:
     valueFrom: "AVG(GQ)>20"
   - valueFrom: "-Ov"
   - prefix: "-o"
-    valueFrom: $(inputs.samplename).vcf
+    valueFrom: $(inputs.sample).vcf
   - {valueFrom: '&&', shellQuote: false}
   - bgzip
-  - valueFrom: $(inputs.samplename).vcf
+  - valueFrom: $(inputs.sample).vcf
   - {valueFrom: '&&', shellQuote: false}
   - tabix
-  - valueFrom: $(inputs.samplename).vcf.gz
+  - valueFrom: $(inputs.sample).vcf.gz
+
+s:codeRepository: https://github.com/arvados/arvados-tutorial
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl