sample:
type: string
label: Sample Name
- knownsites:
+ knownsites1:
type: File
format: edam:format_3016 # VCF
label: VCF of known polymorphic sites for BQSR
secondaryFiles:
- - .tbi
+ - .idx
+ knownsites2:
+ type: File
+ format: edam:format_3016 # VCF
+ label: VCF of known polymorphic sites for BQSR
+ secondaryFiles:
+ - .tbi
scattercount:
type: string
label: Desired split for variant calling
bam: samtools-index/indexedbam
sample: sample
scattercount: scattercount
- knownsites: knownsites
+ knownsites1: knownsites1
+ knownsites2: knownsites2
out: [gatheredgvcf]
generate-report:
run: report-wf.cwl
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
- prefix: "-I"
valueFrom: $(inputs.bam)
- prefix: "--known-sites"
- valueFrom: $(inputs.knownsites)
+ valueFrom: $(inputs.knownsites1)
+ - prefix: "--known-sites"
+ valueFrom: $(inputs.knownsites2)
- prefix: "-L"
valueFrom: $(inputs.intervallist)
- prefix: "-O"
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
bam: bam
reference: reference
sample: sample
- knownsites: knownsites
+ knownsites1: knownsites1
+ knownsites2: knownsites2
intervallist: intervallist
out: [recaltable]
applyBQSR:
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
bam: bam
reference: reference
sample: sample
- knownsites: knownsites
+ knownsites1: knownsites1
+ knownsites2: knownsites2
intervallist: splitintervals/intervalfiles
out: [gvcf]
- ^.dict
fullintervallist:
type: File
- knownsites:
+ 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:
- - .tbi
+ - .idx
+ knownsites2:
+ type: File
+ format: edam:format_3016 # VCF
+ label: VCF of known indel sites for BQSR
+ secondaryFiles:
+ - .tbi
scattercount:
type: string
label: Desired split for variant calling
reference: reference
fullintervallist: fullintervallist
sample: getfastq/sample
- knownsites: knownsites
+ knownsites1: knownsites1
+ knownsites2: knownsites2
scattercount: scattercount
clinvarvcf: clinvarvcf
reportfunc: reportfunc
scattercount: '20'
-knownsites:
+knownsites1:
+ class: File
+ format: edam:format_3016
+ location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.dbsnp138.vcf
+
+knownsites2:
class: File
format: edam:format_3016
location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz