cwlVersion: v1.1
class: CommandLineTool
-label: Annotating and Filtering VCF
+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: $(inputs.vcf.nameroot).txt
inputs:
vcf:
type: File
+ format: edam:format_3016 # VCF
+ label: VCF extracted from GVCF
+ secondaryFiles: [.tbi]
clinvarvcf:
type: File
+ format: edam:format_3016 # VCF
+ label: Reference VCF for ClinVar
+
outputs:
reporttxt: stdout
- query
- prefix: "-f"
valueFrom: "%ID\t%CHROM\t%POS\t%REF\t%ALT\t%INFO/ALLELEID\t%INFO/CLNSIG\t%INFO/CLNDN\t%INFO/AF_ESP\t%INFO/AF_EXAC\t%INFO/AF_TGP[\t%GT]\n"
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl