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cwlVersion: v1.1
class: CommandLineTool
inputs:
readsFA: File
outputs:
readsPAF: stdout
requirements:
InlineJavascriptRequirement: {}
hints:
DockerRequirement:
dockerPull: "quay.io/biocontainers/minimap2:2.17--h8b12597_1"
ResourceRequirement:
coresMin: 8
coresMax: 32
ramMin: $(15 * 1024)
outdirMin: $(Math.ceil(inputs.readsFA.size/(1024*1024*1024) + 20))
stdout: $(inputs.readsFA.nameroot).paf
baseCommand: minimap2
arguments: [-cx, asm20,
-w, "1",
-t, $(runtime.cores),
$(inputs.readsFA),
$(inputs.readsFA)]
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