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Updating cwl and yml for intervals and other changes
[arvados-tutorial.git]
/
WGS-processing
/
cwl
/
helper
/
gatk-splitintervals.cwl
diff --git
a/WGS-processing/cwl/helper/gatk-splitintervals.cwl
b/WGS-processing/cwl/helper/gatk-splitintervals.cwl
index 98758d1e9e5474c4cb8e2cd7dd6aed3c9af12ee3..4909bc7412d0ebfcf64d12f652604d6a556a8da9 100644
(file)
--- a/
WGS-processing/cwl/helper/gatk-splitintervals.cwl
+++ b/
WGS-processing/cwl/helper/gatk-splitintervals.cwl
@@
-32,6
+32,9
@@
inputs:
- .sa
- .fai
- ^.dict
- .sa
- .fai
- ^.dict
+ fullintervallist:
+ type: File
+ label: Full list of intervals to operate over
sample:
type: string
label: Sample Name
sample:
type: string
label: Sample Name
@@
-54,6
+57,8
@@
arguments:
- SplitIntervals
- prefix: "-R"
valueFrom: $(inputs.reference)
- SplitIntervals
- prefix: "-R"
valueFrom: $(inputs.reference)
+ - prefix: "-L"
+ valueFrom: $(inputs.fullintervallist)
- prefix: "--scatter-count"
valueFrom: $(inputs.scattercount)
- prefix: "--subdivision-mode"
- prefix: "--scatter-count"
valueFrom: $(inputs.scattercount)
- prefix: "--subdivision-mode"