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Bugfix .bai secondary file for ApplyBSQR behavior
[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 75c605b822bf07b8fca8e3e66edc4e152153c014..7e48e04d135b9640ac64479138cc01d9822149ab 100644
(file)
--- a/
WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl
+++ b/
WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl
@@
-3,8
+3,8
@@
class: Workflow
label: Scattered variant calling workflow
requirements:
label: Scattered variant calling workflow
requirements:
- - class: SubworkflowFeatureRequirement
- - class: ScatterFeatureRequirement
+ SubworkflowFeatureRequirement: {}
+ ScatterFeatureRequirement: {}
inputs:
bam:
inputs:
bam:
@@
-25,13
+25,22
@@
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
- knownsites:
+ knownsites1:
+ type: File
+ format: edam:format_3016 # VCF
+ label: VCF of known SNPS sites for BQSR
+ secondaryFiles:
+ - .idx
+ knownsites2:
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
indel
sites for BQSR
secondaryFiles:
- .tbi
scattercount:
secondaryFiles:
- .tbi
scattercount:
@@
-52,6
+61,7
@@
steps:
run: gatk-splitintervals.cwl
in:
reference: reference
run: gatk-splitintervals.cwl
in:
reference: reference
+ fullintervallist: fullintervallist
sample: sample
scattercount: scattercount
out: [intervalfiles]
sample: sample
scattercount: scattercount
out: [intervalfiles]
@@
-63,7
+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]