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Removing white spaces and commenting schemas
[arvados-tutorial.git]
/
WGS-processing
/
cwl
/
helper
/
bwamem-samtools-view.cwl
diff --git
a/WGS-processing/cwl/helper/bwamem-samtools-view.cwl
b/WGS-processing/cwl/helper/bwamem-samtools-view.cwl
index 0ad81840545acc43bcade1875b554fa0a4086859..32eb5ce0ab53cfbc4b421905ba59bff2b52df716 100644
(file)
--- a/
WGS-processing/cwl/helper/bwamem-samtools-view.cwl
+++ b/
WGS-processing/cwl/helper/bwamem-samtools-view.cwl
@@
-8,11
+8,11
@@
requirements:
ShellCommandRequirement: {}
ResourceRequirement:
ramMin: 50000
ShellCommandRequirement: {}
ResourceRequirement:
ramMin: 50000
- coresMin: 16
+ coresMin: 16
hints:
arv:RuntimeConstraints:
hints:
arv:RuntimeConstraints:
- keep_cache: 1024
+ keep_cache: 1024
outputDirType: keep_output_dir
SoftwareRequirement:
packages:
outputDirType: keep_output_dir
SoftwareRequirement:
packages:
@@
-36,15
+36,15
@@
inputs:
- .sa
- .fai
- ^.dict
- .sa
- .fai
- ^.dict
- fastq1:
+ fastq1:
type: File
format: edam:format_1930 # FASTQ
label: One of set of pair-end FASTQs (R1)
type: File
format: edam:format_1930 # FASTQ
label: One of set of pair-end FASTQs (R1)
- fastq2:
+ fastq2:
type: File
format: edam:format_1930 # FASTQ
label: One of set of pair-end FASTQs (R2)
type: File
format: edam:format_1930 # FASTQ
label: One of set of pair-end FASTQs (R2)
- sample:
+ sample:
type: string
label: Sample Name
type: string
label: Sample Name
@@
-66,7
+66,7
@@
arguments:
- $(runtime.cores)
- $(inputs.reference)
- -R
- $(runtime.cores)
- $(inputs.reference)
- -R
- - '@RG\tID:sample\tSM:sample\tLB:sample\tPL:ILLUMINA\tPU:sample1'
+ - '@RG\tID:sample\tSM:sample\tLB:sample\tPL:ILLUMINA\tPU:sample1'
- -c
- '250'
- $(inputs.fastq1)
- -c
- '250'
- $(inputs.fastq1)
@@
-91,6
+91,6
@@
$namespaces:
arv: "http://arvados.org/cwl#"
cwltool: "http://commonwl.org/cwltool#"
arv: "http://arvados.org/cwl#"
cwltool: "http://commonwl.org/cwltool#"
-$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