Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #
bam: samtools-index/indexedbam
sample: sample
scattercount: scattercount
bam: samtools-index/indexedbam
sample: sample
scattercount: scattercount
- knownsites1: knownsites
out: [gatheredgvcf]
generate-report:
run: report-wf.cwl
out: [gatheredgvcf]
generate-report:
run: report-wf.cwl
sample:
type: string
label: Sample Name
sample:
type: string
label: Sample Name
type: File
format: edam:format_3016 # VCF
label: VCF of known polymorphic sites for BQSR
type: File
format: edam:format_3016 # VCF
label: VCF of known polymorphic sites for BQSR
- prefix: "-I"
valueFrom: $(inputs.bam.basename)
- prefix: "--known-sites"
- prefix: "-I"
valueFrom: $(inputs.bam.basename)
- prefix: "--known-sites"
- valueFrom: $(inputs.knownsites1)
+ valueFrom: $(inputs.knownsites)
- prefix: "-L"
valueFrom: $(inputs.intervallist)
- prefix: "-O"
- prefix: "-L"
valueFrom: $(inputs.intervallist)
- prefix: "-O"
sample:
type: string
label: Sample Name
sample:
type: string
label: Sample Name
type: File
format: edam:format_3016 # VCF
label: VCF of known polymorphic sites for BQSR
type: File
format: edam:format_3016 # VCF
label: VCF of known polymorphic sites for BQSR
bam: bam
reference: reference
sample: sample
bam: bam
reference: reference
sample: sample
- knownsites1: knownsites1
intervallist: intervallist
out: [recaltable]
applyBQSR:
intervallist: intervallist
out: [recaltable]
applyBQSR:
sample:
type: string
label: Sample Name
sample:
type: string
label: Sample Name
type: File
format: edam:format_3016 # VCF
label: VCF of known polymorphic sites for BQSR
type: File
format: edam:format_3016 # VCF
label: VCF of known polymorphic sites for BQSR
bam: bam
reference: reference
sample: sample
bam: bam
reference: reference
sample: sample
- knownsites1: knownsites1
intervallist: splitintervals/intervalfiles
out: [gvcf]
intervallist: splitintervals/intervalfiles
out: [gvcf]