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Updating to allow for two vcfs of known sites
[arvados-tutorial.git]
/
WGS-processing
/
cwl
/
helper
/
gatk-baserecalibrator-with-interval.cwl
diff --git
a/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
b/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
index 7ae08377f143563bd425ed4314d4b7af8d5a8d39..2de30a62b88d0a0923b6951eaa05b9cf31c0ddc2 100644
(file)
--- a/
WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
+++ b/
WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
@@
-41,7
+41,13
@@
inputs:
sample:
type: string
label: Sample Name
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
type: File
format: edam:format_3016 # VCF
label: VCF of known polymorphic sites for BQSR
@@
-69,7
+75,9
@@
arguments:
- prefix: "-I"
valueFrom: $(inputs.bam)
- prefix: "--known-sites"
- 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"
- prefix: "-L"
valueFrom: $(inputs.intervallist)
- prefix: "-O"