projects
/
arvados-tutorial.git
/ blobdiff
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Updating to allow for two vcfs of known sites
[arvados-tutorial.git]
/
WGS-processing
/
cwl
/
helper
/
scatter-gatk-wf-with-interval.cwl
diff --git
a/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl
b/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl
index 80d7601115c8ef2cb1839e273266cdc1947ce4dd..13bd4af04c3528e384078e073c4e722823e498ec 100644
(file)
--- a/
WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl
+++ b/
WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl
@@
-31,7
+31,13
@@
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
@@
-67,7
+73,8
@@
steps:
bam: bam
reference: reference
sample: sample
bam: bam
reference: reference
sample: sample
- knownsites: knownsites
+ knownsites1: knownsites1
+ knownsites2: knownsites2
intervallist: splitintervals/intervalfiles
out: [gvcf]
intervallist: splitintervals/intervalfiles
out: [gvcf]