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Removing white spaces and commenting schemas
[arvados-tutorial.git]
/
WGS-processing
/
cwl
/
helper
/
gatk-selectvariants.cwl
diff --git
a/WGS-processing/cwl/helper/gatk-selectvariants.cwl
b/WGS-processing/cwl/helper/gatk-selectvariants.cwl
index 8e7031abe7581905650ac2cd220689357856aaf5..bb5643b50b077ec25467ee8c49f7dd0dfc4343c8 100644
(file)
--- a/
WGS-processing/cwl/helper/gatk-selectvariants.cwl
+++ b/
WGS-processing/cwl/helper/gatk-selectvariants.cwl
@@
-38,7
+38,7
@@
inputs:
- .sa
- .fai
- ^.dict
- .sa
- .fai
- ^.dict
- sample:
+ sample:
type: string
label: Sample Name
type: string
label: Sample Name
@@
-46,7
+46,7
@@
outputs:
filteredgvcf:
type: File
format: edam:format_3016 # GVCF
filteredgvcf:
type: File
format: edam:format_3016 # GVCF
- label: Given interval filtered GVCF
+ label: Given interval filtered GVCF
outputBinding:
glob: "*g.vcf.gz"
outputBinding:
glob: "*g.vcf.gz"
@@
-55,7
+55,7
@@
baseCommand: /gatk/gatk
arguments:
- "--java-options"
- "-Xmx4G"
arguments:
- "--java-options"
- "-Xmx4G"
- - SelectVariants
+ - SelectVariants
- prefix: "-R"
valueFrom: $(inputs.reference)
- prefix: "--remove-unused-alternates"
- prefix: "-R"
valueFrom: $(inputs.reference)
- prefix: "--remove-unused-alternates"
@@
-74,6
+74,6
@@
$namespaces:
arv: "http://arvados.org/cwl#"
cwltool: "http://commonwl.org/cwltool#"
arv: "http://arvados.org/cwl#"
cwltool: "http://commonwl.org/cwltool#"
-$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