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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 d740222db6e399a993ffb81d1767d80ba001426f..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
@@
-1,10
+1,10
@@
cwlVersion: v1.1
class: Workflow
cwlVersion: v1.1
class: Workflow
-label:
Variant calling workflow scattered over interval splits
+label:
Scattered variant calling workflow
requirements:
requirements:
- - class: SubworkflowFeatureRequirement
- - class: ScatterFeatureRequirement
+ SubworkflowFeatureRequirement: {}
+ ScatterFeatureRequirement: {}
inputs:
bam:
inputs:
bam:
@@
-25,16
+25,25
@@
inputs:
- .sa
- .fai
- ^.dict
- .sa
- .fai
- ^.dict
- sample:
+ fullintervallist:
+ type: File
+ label: Full list of intervals to operate over
+ 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
secondaryFiles:
- .tbi
type: File
format: edam:format_3016 # VCF
label: VCF of known polymorphic sites for BQSR
secondaryFiles:
- .tbi
- scattercount:
+ scattercount:
type: string
label: Desired split for variant calling
type: string
label: Desired split for variant calling
@@
-42,21
+51,22
@@
outputs:
gatheredgvcf:
type: File
format: edam:format_3016 # GVCF
gatheredgvcf:
type: File
format: edam:format_3016 # GVCF
- label: G
VCF generated from GATK Haplotype Caller
- secondaryFiles:
+ label: G
athered GVCF
+ secondaryFiles:
- .tbi
- .tbi
- outputSource:
merge
-GVCFs/gatheredgvcf
+ outputSource:
gather
-GVCFs/gatheredgvcf
steps:
splitintervals:
run: gatk-splitintervals.cwl
in:
reference: reference
steps:
splitintervals:
run: gatk-splitintervals.cwl
in:
reference: reference
+ fullintervallist: fullintervallist
sample: sample
scattercount: scattercount
out: [intervalfiles]
sample: sample
scattercount: scattercount
out: [intervalfiles]
- recal-haplotypecaller:
+ recal-haplotypecaller:
run: gatk-wf-with-interval.cwl
scatter: intervallist
in:
run: gatk-wf-with-interval.cwl
scatter: intervallist
in:
@@
-64,16
+74,17
@@
steps:
reference: reference
sample: sample
knownsites1: knownsites1
reference: reference
sample: sample
knownsites1: knownsites1
+ knownsites2: knownsites2
intervallist: splitintervals/intervalfiles
out: [gvcf]
intervallist: splitintervals/intervalfiles
out: [gvcf]
-
merge
-GVCFs:
+
gather
-GVCFs:
run: gather-array-vcf.cwl
in:
gvcfarray: recal-haplotypecaller/gvcf
sample: sample
reference: reference
run: gather-array-vcf.cwl
in:
gvcfarray: recal-haplotypecaller/gvcf
sample: sample
reference: reference
- out: [gatheredgvcf]
+ out: [gatheredgvcf]
s:codeRepository: https://github.com/arvados/arvados-tutorial
s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
s:codeRepository: https://github.com/arvados/arvados-tutorial
s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
@@
-82,6
+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