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: curii/fastqc
   8   InitialWorkDirRequirement:
   9     listing:
  10       - $(inputs.fastq1)
  11       - $(inputs.fastq2)
  12
  13 hints:
  14   SoftwareRequirement:
  15     packages:
  16       FastQC:
  17         specs: [ "https://identifiers.org/rrid/RRID:SCR_014583" ]
  18         version: [ "0.11.9" ]
  19
  20 inputs:
  21   fastq1:
  22     type: File
  23     format: edam:format_1930 # FASTQ
  24     label: One of set of pair-end FASTQs (R1)
  25   fastq2:
  26     type: File
  27     format: edam:format_1930 # FASTQ
  28     label: One of set of pair-end FASTQs (R2)
  29
  30 outputs:
  31   out-html:
  32     type: File[]
  33     label: FASTQ QC reports
  34     format: edam:format_1964 # HTML
  35     outputBinding:
  36       glob: "*html"
  37   out-zip:
  38     type: File[]
  39     label: Zip files of FASTQ QC report and associated data
  40     outputSource: fastqc/out-zip
  41     outputBinding:
  42       glob: "*fastqc.zip"
  43
  44 baseCommand: perl
  45
  46 arguments:
  47   - /FastQC/fastqc
  48   - $(inputs.fastq1.basename)
  49   - $(inputs.fastq2.basename)
  50
  51 s:codeRepository: https://github.com/arvados/arvados-tutorial
  52 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
  53
  54 $namespaces:
  55  s: https://schema.org/
  56  edam: http://edamontology.org/
  57
  58 $schemas:
  59  - https://schema.org/version/latest/schema.rdf
  60  - http://edamontology.org/EDAM_1.18.owl