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Bugfix .bai secondary file for ApplyBSQR behavior
[arvados-tutorial.git]
/
WGS-processing
/
cwl
/
helper
/
gatk-haplotypecaller-with-interval.cwl
diff --git
a/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl
b/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl
index 22ce3f6b8a3521d6bca2308b91dfb8b3949f5835..0b6c1029ddc3f135ec39fbb834587906f336ffe3 100644
(file)
--- a/
WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl
+++ b/
WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl
@@
-9,10
+9,10
@@
requirements:
hints:
arv:RuntimeConstraints:
outputDirType: keep_output_dir
hints:
arv:RuntimeConstraints:
outputDirType: keep_output_dir
- keep_cache: 1024
+ keep_cache: 1024
ResourceRequirement:
ramMin: 3500
ResourceRequirement:
ramMin: 3500
- coresMin: 2
+ coresMin: 2
SoftwareRequirement:
packages:
GATK:
SoftwareRequirement:
packages:
GATK:
@@
-25,7
+25,7
@@
inputs:
format: edam:format_2572 # BAM
label: Recalibrated BAM for given interval
secondaryFiles:
format: edam:format_2572 # BAM
label: Recalibrated BAM for given interval
secondaryFiles:
- - .bai
+ -
^
.bai
reference:
type: File
format: edam:format_1929 # FASTA
reference:
type: File
format: edam:format_1929 # FASTA
@@
-41,7
+41,7
@@
inputs:
intervallist:
type: File
label: Scatter intervals file
intervallist:
type: File
label: Scatter intervals file
- sample:
+ sample:
type: string
label: Sample Name
type: string
label: Sample Name
@@
-68,7
+68,7
@@
arguments:
- prefix: "-L"
valueFrom: $(inputs.intervallist)
- prefix: "-O"
- prefix: "-L"
valueFrom: $(inputs.intervallist)
- prefix: "-O"
- valueFrom: $(
runtime.outdir)/$(
inputs.sample)-$(inputs.intervallist.nameroot).gatk.g.vcf.gz
+ valueFrom: $(inputs.sample)-$(inputs.intervallist.nameroot).gatk.g.vcf.gz
- prefix: "-ERC"
valueFrom: "GVCF"
- prefix: "-GQB"
- prefix: "-ERC"
valueFrom: "GVCF"
- prefix: "-GQB"
@@
-87,6
+87,6
@@
$namespaces:
arv: "http://arvados.org/cwl#"
cwltool: "http://commonwl.org/cwltool#"
arv: "http://arvados.org/cwl#"
cwltool: "http://commonwl.org/cwltool#"
-$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