- .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
secondaryFiles:
- - .tbi
+ - .tbi
scattercount:
type: string
label: Desired split for variant calling
run: scatter-gatk-wf-with-interval.cwl
in:
reference: reference
+ fullintervallist: fullintervallist
bam: samtools-index/indexedbam
sample: sample
scattercount: scattercount
- knownsites: knownsites
+ knownsites1: knownsites1
+ knownsites2: knownsites2
out: [gatheredgvcf]
generate-report:
run: report-wf.cwl