label: Scattered variant calling workflow
requirements:
- - class: SubworkflowFeatureRequirement
- - class: ScatterFeatureRequirement
+ SubworkflowFeatureRequirement: {}
+ ScatterFeatureRequirement: {}
inputs:
bam:
- .sa
- .fai
- ^.dict
+ fullintervallist:
+ type: File
+ label: Full list of intervals to operate over
sample:
type: string
label: Sample Name
- knownsites:
+ knownsites1:
+ type: File
+ format: edam:format_3016 # VCF
+ label: VCF of known polymorphic sites for BQSR
+ secondaryFiles:
+ - .idx
+ knownsites2:
type: File
format: edam:format_3016 # VCF
label: VCF of known polymorphic sites for BQSR
run: gatk-splitintervals.cwl
in:
reference: reference
+ fullintervallist: fullintervallist
sample: sample
scattercount: scattercount
out: [intervalfiles]
bam: bam
reference: reference
sample: sample
- knownsites: knownsites
+ knownsites1: knownsites1
+ knownsites2: knownsites2
intervallist: splitintervals/intervalfiles
out: [gvcf]