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cwlVersion: v1.1
class: CommandLineTool
inputs:
inputGFA: File
outputs:
odgiGraph:
type: File
outputBinding:
glob: $(inputs.inputGFA.nameroot).unchop.sorted.odgi
requirements:
InlineJavascriptRequirement: {}
hints:
DockerRequirement:
dockerPull: "odgi-bash-binutils:latest"
ResourceRequirement:
coresMin: 4
ramMin: $(7 * 1024)
outdirMin: $(Math.ceil((inputs.inputGFA.size/(1024*1024*1024)+1) * 2))
InitialWorkDirRequirement:
# Will fail if input file is not writable (odgi bug)
listing:
- entry: $(inputs.inputGFA)
writable: true
arguments:
- "sh"
- "-c"
- >-
odgi build -g '$(inputs.inputGFA.path)' -o - | odgi unchop -i - -o - |
odgi sort -i - -p s -o $(inputs.inputGFA.nameroot).unchop.sorted.odgi
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