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Switching variable knownsites1 to knownsites
[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 7e5bf4df4bc863807a4136547ab794af374cb69e..6df9de12675d1a00af561adb2d874376c9cf4801 100644
(file)
--- a/
WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
+++ b/
WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
@@
-44,7
+44,7
@@
inputs:
sample:
type: string
label: Sample Name
sample:
type: string
label: Sample Name
- knownsites
1
:
+ knownsites:
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
@@
-72,7
+72,7
@@
arguments:
- prefix: "-I"
valueFrom: $(inputs.bam.basename)
- prefix: "--known-sites"
- prefix: "-I"
valueFrom: $(inputs.bam.basename)
- prefix: "--known-sites"
- valueFrom: $(inputs.knownsites
1
)
+ valueFrom: $(inputs.knownsites)
- prefix: "-L"
valueFrom: $(inputs.intervallist)
- prefix: "-O"
- prefix: "-L"
valueFrom: $(inputs.intervallist)
- prefix: "-O"