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#!/usr/bin/env cwl-runner
cwlVersion: v1.1
class: CommandLineTool
baseCommand: pggb
inputs:
threads:
type: int
inputBinding:
position: 1
prefix: -t
pggb_wfmash:
type: boolean
inputBinding:
position: 2
prefix: --wfmash
pggb_fasta:
type: File
inputBinding:
position: 3
prefix: -i
pggb_mash_k_mer:
type: int
inputBinding:
position: 4
prefix: -K
pggb_map_percent_identity:
type: int
inputBinding:
position: 5
prefix: -p
pggb_num_secondary_mappings:
type: int
inputBinding:
position: 6
prefix: -n
pggb_segment_length:
type: int
inputBinding:
position: 7
prefix: -s
pggb_output_dir:
type: string
inputBinding:
position: 8
prefix: -o
outputs:
pggb_odgi_graph:
type: File
outputBinding:
glob: '*.smooth.og'
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