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Updating to allow for two vcfs of known sites
[arvados-tutorial.git]
/
WGS-processing
/
cwl
/
helper
/
gatk-wf-with-interval.cwl
diff --git
a/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
b/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
index de4a648e8a90cd08a697203e205e931a95be8b1c..d9023c92186ca6fda034cbf4552accdb5c069364 100644
(file)
--- a/
WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
+++ b/
WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
@@
-27,7
+27,13
@@
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
@@
-51,7
+57,8
@@
steps:
bam: bam
reference: reference
sample: sample
bam: bam
reference: reference
sample: sample
- knownsites: knownsites
+ knownsites1: knownsites1
+ knownsites2: knownsites2
intervallist: intervallist
out: [recaltable]
applyBQSR:
intervallist: intervallist
out: [recaltable]
applyBQSR: