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Updating to allow for two vcfs of known sites
[arvados-tutorial.git]
/
WGS-processing
/
cwl
/
wgs-processing-wf.cwl
diff --git
a/WGS-processing/cwl/wgs-processing-wf.cwl
b/WGS-processing/cwl/wgs-processing-wf.cwl
index 8cbcf5ee03b17f7d5800b611fd29a4d69cfcc105..8499b92bdbedbc119abc8dd45dab04a39b827703 100644
(file)
--- a/
WGS-processing/cwl/wgs-processing-wf.cwl
+++ b/
WGS-processing/cwl/wgs-processing-wf.cwl
@@
-24,12
+24,18
@@
inputs:
- ^.dict
fullintervallist:
type: File
- ^.dict
fullintervallist:
type: File
- knownsites:
+ knownsites
1
:
type: File
format: edam:format_3016 # VCF
type: File
format: edam:format_3016 # VCF
- label: VCF of known
polymorphic
sites for BQSR
+ label: VCF of known
SNPS
sites for BQSR
secondaryFiles:
secondaryFiles:
- - .tbi
+ - .idx
+ knownsites2:
+ type: File
+ format: edam:format_3016 # VCF
+ label: VCF of known indel sites for BQSR
+ secondaryFiles:
+ - .tbi
scattercount:
type: string
label: Desired split for variant calling
scattercount:
type: string
label: Desired split for variant calling
@@
-78,7
+84,8
@@
steps:
reference: reference
fullintervallist: fullintervallist
sample: getfastq/sample
reference: reference
fullintervallist: fullintervallist
sample: getfastq/sample
- knownsites: knownsites
+ knownsites1: knownsites1
+ knownsites2: knownsites2
scattercount: scattercount
clinvarvcf: clinvarvcf
reportfunc: reportfunc
scattercount: scattercount
clinvarvcf: clinvarvcf
reportfunc: reportfunc