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Adding modified code to select variants and gather arrays
[arvados-tutorial.git]
/
cwl
/
helper
/
samtools-sort.cwl
diff --git
a/cwl/helper/samtools-sort.cwl
b/cwl/helper/samtools-sort.cwl
index b583f66be91d2897efb58f3da911793e9cd3c4c7..02072cdfbf863e0e6f982cd7cb21bb33603a21e2 100644
(file)
--- a/
cwl/helper/samtools-sort.cwl
+++ b/
cwl/helper/samtools-sort.cwl
@@
-10,9
+10,6
@@
requirements:
DockerRequirement:
dockerPull: curii/bwa-samtools-picard
ShellCommandRequirement: {}
DockerRequirement:
dockerPull: curii/bwa-samtools-picard
ShellCommandRequirement: {}
- InitialWorkDirRequirement:
- listing:
- - $(inputs.bam)
ResourceRequirement:
ramMin: 20000
coresMin: 4
ResourceRequirement:
ramMin: 20000
coresMin: 4
@@
-27,7
+24,7
@@
inputs:
sample: string
outputs:
sample: string
outputs:
- bam:
+
sorted
bam:
type: File
outputBinding:
glob: "*sorted.bam"
type: File
outputBinding:
glob: "*sorted.bam"
@@
-38,7
+35,7
@@
arguments:
- sort
- -@
- $(runtime.cores)
- sort
- -@
- $(runtime.cores)
- - $(inputs.bam.
basename
)
+ - $(inputs.bam.
path
)
- -m
- '2G'
- -o
- -m
- '2G'
- -o