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Removing white spaces and commenting schemas
[arvados-tutorial.git]
/
WGS-processing
/
cwl
/
helper
/
gather-vcf.cwl
diff --git
a/WGS-processing/cwl/helper/gather-vcf.cwl
b/WGS-processing/cwl/helper/gather-vcf.cwl
index 15b6551f03d58fed449693976be9e2ba6cdbe654..b59fc351aac0919207ed59f29779ba339dd08c19 100644
(file)
--- a/
WGS-processing/cwl/helper/gather-vcf.cwl
+++ b/
WGS-processing/cwl/helper/gather-vcf.cwl
@@
-15,16
+15,16
@@
requirements:
hints:
ResourceRequirement:
ramMin: 20000
hints:
ResourceRequirement:
ramMin: 20000
- coresMin: 4
+ coresMin: 4
arv:RuntimeConstraints:
outputDirType: keep_output_dir
inputs:
arv:RuntimeConstraints:
outputDirType: keep_output_dir
inputs:
- gvcfdir:
+ gvcfdir:
type: Directory
label: Input directory of GVCFs
loadListing: 'shallow_listing'
type: Directory
label: Input directory of GVCFs
loadListing: 'shallow_listing'
- sample:
+ sample:
type: string
label: Sample Name
reference:
type: string
label: Sample Name
reference:
@@
-43,7
+43,7
@@
outputs:
gatheredgvcf:
type: File
format: edam:format_3016 # GVCF
gatheredgvcf:
type: File
format: edam:format_3016 # GVCF
- label: Gathered GVCF
+ label: Gathered GVCF
secondaryFiles:
- .tbi
outputBinding:
secondaryFiles:
- .tbi
outputBinding:
@@
-53,10
+53,10
@@
baseCommand: /gatk/gatk
arguments:
- "--java-options"
arguments:
- "--java-options"
- - "-Xmx8G"
+ - "-Xmx8G"
- MergeVcfs
- shellQuote: false
- MergeVcfs
- shellQuote: false
- valueFrom: |
+ valueFrom: |
${function compare(a, b) {
var baseA = a.basename;
var baseB = b.basename;
${function compare(a, b) {
var baseA = a.basename;
var baseB = b.basename;
@@
-68,7
+68,7
@@
arguments:
comparison = -1;
}
return comparison;
comparison = -1;
}
return comparison;
- }
+ }
var samples = [];
for (var i = 0; i < inputs.gvcfdir.listing.length; i++) {
var samples = [];
for (var i = 0; i < inputs.gvcfdir.listing.length; i++) {
@@
-99,6
+99,6
@@
$namespaces:
arv: "http://arvados.org/cwl#"
cwltool: "http://commonwl.org/cwltool#"
arv: "http://arvados.org/cwl#"
cwltool: "http://commonwl.org/cwltool#"
-$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