Bugfix .bai secondary file for ApplyBSQR behavior

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

diff --git a/WGS-processing/cwl/helper/annotate-vcf.cwl b/WGS-processing/cwl/helper/annotate-vcf.cwl
index 310753c5c458b849d767e027cae696f8e462576a..1e028c4adebba781620f27671f3e793575804561 100644 (file)
--- a/WGS-processing/cwl/helper/annotate-vcf.cwl
+++ b/WGS-processing/cwl/helper/annotate-vcf.cwl
@@ -3,22 +3,32 @@ class: CommandLineTool
 label: Annotate and filter 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" ]
 
 stdout: $(inputs.vcf.nameroot).txt
 
 inputs:
   vcf:
     type: File
+    format: edam:format_3016 # VCF
+    label: VCF extracted from GVCF
+    secondaryFiles: [.tbi]
   clinvarvcf:
     type: File
+    format: edam:format_3016 # VCF
+    label: Reference VCF for ClinVar
 
 outputs:
   reporttxt: stdout
@@ -41,3 +51,11 @@ arguments:
   - query
   - prefix: "-f"
     valueFrom: "%ID\t%CHROM\t%POS\t%REF\t%ALT\t%INFO/ALLELEID\t%INFO/CLNSIG\t%INFO/CLNDN\t%INFO/AF_ESP\t%INFO/AF_EXAC\t%INFO/AF_TGP[\t%GT]\n"
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl