- .sa
- .fai
- ^.dict
- knownsites:
+ fullintervallist:
+ type: File
+ knownsites1:
+ type: File
+ format: edam:format_3016 # VCF
+ label: VCF of known SNPS sites for BQSR
+ secondaryFiles:
+ - .idx
+ knownsites2:
type: File
format: edam:format_3016 # VCF
- label: VCF of known polymorphic sites for BQSR
+ label: VCF of known indel sites for BQSR
secondaryFiles:
- - .tbi
+ - .tbi
scattercount:
type: string
label: Desired split for variant calling
fastq1: getfastq/fastq1
fastq2: getfastq/fastq2
reference: reference
+ fullintervallist: fullintervallist
sample: getfastq/sample
- knownsites: knownsites
+ knownsites1: knownsites1
+ knownsites2: knownsites2
scattercount: scattercount
clinvarvcf: clinvarvcf
reportfunc: reportfunc