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Updating bwamem CWL and adding base recalibrator cwl
[arvados-tutorial.git]
/
cwl
/
bwamem-samtools-sort.cwl
diff --git
a/cwl/bwamem-samtools-sort.cwl
b/cwl/bwamem-samtools-sort.cwl
index 18ad65cee8db1cba0446f0f8d3d03a7a034b0dc8..2077ebde683d36af3d09abaf5960579ebdd61a72 100644
(file)
--- a/
cwl/bwamem-samtools-sort.cwl
+++ b/
cwl/bwamem-samtools-sort.cwl
@@
-10,12
+10,13
@@
requirements:
dockerPull: curii/bwa-samtools-picard
ShellCommandRequirement: {}
ResourceRequirement:
dockerPull: curii/bwa-samtools-picard
ShellCommandRequirement: {}
ResourceRequirement:
- ramMin: 2
6000
+ ramMin: 2
0000
coresMin: 16
hints:
arv:RuntimeConstraints:
outputDirType: keep_output_dir
coresMin: 16
hints:
arv:RuntimeConstraints:
outputDirType: keep_output_dir
+ keep_cache: 9216
inputs:
reference:
inputs:
reference:
@@
-58,9
+59,9
@@
arguments:
- samtools
- sort
- -@
- samtools
- sort
- -@
- -
$(runtime.cores)
+ -
'16'
- -m
- -m
- - '
2G
'
+ - '
500M
'
- -l
- '6'
- -o
- -l
- '6'
- -o