WGS-processing/cwl/helper/fastqc.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Quality check on FASTQ
   4
   5 requirements:
   6   DockerRequirement:
   7     dockerPull: biocontainers/fastqc:v0.11.9_cv6
   8
   9 hints:
  10   SoftwareRequirement:
  11     packages:
  12       FastQC:
  13         specs: [ "https://identifiers.org/rrid/RRID:SCR_014583" ]
  14         version: [ "0.11.9" ]
  15
  16 inputs:
  17   fastq1:
  18     type: File
  19     format: edam:format_1930 # FASTQ
  20     label: One of set of pair-end FASTQs (R1)
  21   fastq2:
  22     type: File
  23     format: edam:format_1930 # FASTQ
  24     label: One of set of pair-end FASTQs (R2)
  25
  26 outputs:
  27   out-html:
  28     type: File[]
  29     label: FASTQ QC reports
  30     format: edam:format_2331 # HTML
  31     outputBinding:
  32       glob: "*html"
  33   out-zip:
  34     type: File[]
  35     label: Zip files of FASTQ QC report and associated data
  36     outputBinding:
  37       glob: "*fastqc.zip"
  38
  39 baseCommand: fastqc
  40
  41 arguments:
  42   - $(inputs.fastq1.path)
  43   - $(inputs.fastq2.path)
  44
  45 s:codeRepository: https://github.com/arvados/arvados-tutorial
  46 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
  47
  48 $namespaces:
  49  s: https://schema.org/
  50  edam: http://edamontology.org/
  51
  52 #$schemas:
  53 # - https://schema.org/version/latest/schema.rdf
  54 # - http://edamontology.org/EDAM_1.18.owl