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cwlVersion: v1.1
class: CommandLineTool
inputs:
readsFA: File
readsPAF: File
kmerSize:
type: int
default: 16
outputs:
seqwishGFA:
type: File
outputBinding:
glob: $(inputs.readsPAF.nameroot).gfa
requirements:
InlineJavascriptRequirement: {}
hints:
DockerRequirement:
dockerPull: "quay.io/biocontainers/seqwish:0.4.1--h8b12597_0"
ResourceRequirement:
coresMin: 4
ramMin: $(7 * 1024)
outdirMin: $(Math.ceil(inputs.readsFA.size/(1024*1024*1024) + 20))
stdout: $(inputs.readsFA.nameroot).paf
baseCommand: seqwish
arguments: [-t, $(runtime.cores),
-k, $(inputs.kmerSize),
-s, $(inputs.readsFA),
-p, $(inputs.readsPAF),
-g, $(inputs.readsPAF.nameroot).gfa]
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