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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 ef902099c066015699866acad47b4129da3ffcc1..d9023c92186ca6fda034cbf4552accdb5c069364 100644
(file)
--- a/
WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
+++ b/
WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
@@
-1,9
+1,9
@@
cwlVersion: v1.1
class: Workflow
cwlVersion: v1.1
class: Workflow
-label: Variant calling workflow for
single interval
+label: Variant calling workflow for
given interval
requirements:
requirements:
- - class: SubworkflowFeatureRequirement
+ SubworkflowFeatureRequirement: {}
inputs:
bam:
inputs:
bam:
@@
-24,10
+24,16
@@
inputs:
- .sa
- .fai
- ^.dict
- .sa
- .fai
- ^.dict
- sample:
+ sample:
type: string
label: Sample Name
knownsites1:
type: string
label: Sample Name
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
@@
-35,13
+41,13
@@
inputs:
- .tbi
intervallist:
type: File
- .tbi
intervallist:
type: File
- label: Scatter intervals file
+ label: Scatter intervals file
outputs:
gvcf:
type: File
format: edam:format_3016 # GVCF
outputs:
gvcf:
type: File
format: edam:format_3016 # GVCF
- label:
single
interval filtered GVCF
+ label:
Given
interval filtered GVCF
outputSource: selectvariants/filteredgvcf
steps:
outputSource: selectvariants/filteredgvcf
steps:
@@
-52,11
+58,12
@@
steps:
reference: reference
sample: sample
knownsites1: knownsites1
reference: reference
sample: sample
knownsites1: knownsites1
+ knownsites2: knownsites2
intervallist: intervallist
out: [recaltable]
applyBQSR:
run: gatk-applyBSQR-with-interval.cwl
intervallist: intervallist
out: [recaltable]
applyBQSR:
run: gatk-applyBSQR-with-interval.cwl
- in:
+ in:
reference: reference
bam: bam
sample: sample
reference: reference
bam: bam
sample: sample
@@
-73,7
+80,7
@@
steps:
out: [gvcf]
selectvariants:
run: gatk-selectvariants.cwl
out: [gvcf]
selectvariants:
run: gatk-selectvariants.cwl
- in:
+ in:
gvcf: haplotypecaller/gvcf
reference: reference
sample: sample
gvcf: haplotypecaller/gvcf
reference: reference
sample: sample
@@
-86,6
+93,6
@@
$namespaces:
s: https://schema.org/
edam: http://edamontology.org/
s: https://schema.org/
edam: http://edamontology.org/
-$schemas:
- - https://schema.org/version/latest/schema.rdf
- - http://edamontology.org/EDAM_1.18.owl
+
#
$schemas:
+
#
- https://schema.org/version/latest/schema.rdf
+
#
- http://edamontology.org/EDAM_1.18.owl