fastp (single-end) cwl tool

fastp_se.cwl

cwlVersion: v1.0
class: CommandLineTool

hints:
  DockerRequirement:
    dockerPull: quay.io/biocontainers/fastp:0.20.1--h8b12597_0

baseCommand: fastp

inputs:
  in1:
    label: "read1 input file name"
    type: File
    inputBinding:
      prefix: -i
  out1:
    label: "read1 output file name"
    type: string
    default: clean.fasta
    inputBinding:
      prefix: -o
  html:
    label: "the html format report file name"
    type: string
    inputBinding:
      prefix: -h
  json:
    label: "the json format report file name"
    type: string
    inputBinding:
      prefix: -j

outputs:
  clean_seq:
    type: File
    outputBinding:
      glob: $(inputs.out1)
  html_report:
    type: File
    outputBinding:
      glob: $(inputs.html)
  json_report:
    type: File
    outputBinding:
       glob: $(inputs.json)