cwlVersion: v1.1
class: CommandLineTool
-label: Generate recalibration table for BQSR
+label: Generate recalibration table for BQSR
requirements:
DockerRequirement:
dockerPull: broadinstitute/gatk:4.1.7.0
- InitialWorkDirRequirement:
- listing:
- - $(inputs.bam)
hints:
arv:RuntimeConstraints:
sample:
type: string
label: Sample Name
- knownsites1:
+ knownsites1:
type: File
format: edam:format_3016 # VCF
- label: VCF of known polymorphic sites for BQSR
+ label: VCF of known SNPS sites for BQSR
+ secondaryFiles:
+ - .idx
+ knownsites2:
+ type: File
+ format: edam:format_3016 # VCF
+ label: VCF of known indel sites for BQSR
secondaryFiles:
- .tbi
intervallist:
outputs:
recaltable:
type: File
- label: Recalibration table
+ label: Recalibration table for given interval
outputBinding:
glob: "*.table"
- prefix: "-R"
valueFrom: $(inputs.reference)
- prefix: "-I"
- valueFrom: $(inputs.bam.basename)
+ valueFrom: $(inputs.bam)
- prefix: "--known-sites"
valueFrom: $(inputs.knownsites1)
+ - prefix: "--known-sites"
+ valueFrom: $(inputs.knownsites2)
- prefix: "-L"
valueFrom: $(inputs.intervallist)
- prefix: "-O"
arv: "http://arvados.org/cwl#"
cwltool: "http://commonwl.org/cwltool#"
-$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