Commit eeae5fef authored by Nijsse, Bart's avatar Nijsse, Bart
Browse files

added memory option

parent a21c2407
......@@ -26,6 +26,11 @@ inputs:
inputBinding:
prefix: --threads
default: 2
memory:
type: int?
doc: maximum memory usage in megabytes
label: memory usage (mb)
default: 8000
assembly:
type: File
......@@ -40,8 +45,8 @@ inputs:
doc: Indexed sorted bam file with mapped reads to draft assembly
inputBinding:
prefix: --frags
secondaryFiles:
- .bai
# secondaryFiles:
# - .bai
fixlist:
type: string?
label: Fix List
......@@ -63,10 +68,12 @@ inputs:
inputBinding:
prefix: --vcf
baseCommand: ["java", "-jar","/unlock/infrastructure/binaries/Pilon/pilon-1.24.jar"]
baseCommand: ["java"]
arguments:
- "-jar"
- "-Xmx$(inputs.memory)M"
- "/unlock/infrastructure/binaries/Pilon/pilon-1.24.jar"
- valueFrom: $(inputs.identifier)_scaffolds_polished
prefix: "--output"
......
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