blog-examples/debugging/fastqc/fastqc_blog.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   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     label: One of set of pair-end FASTQs (R1)
  24
  25   fastq2:
  26     type: File
  27     label: One of set of pair-end FASTQs (R2)
  28
  29 outputs:
  30   out-html:
  31     type: File[]
  32     label: FASTQ QC reports
  33     outputBinding:
  34       glob: "*html"
  35   out-zip:
  36     type: File[]
  37     label: Zip files of FASTQ QC report and associated data
  38     outputBinding:
  39       glob: "*fastqc.zip"
  40
  41 baseCommand: fastqc
  42
  43 arguments:
  44   - "--noextract"
  45   - $(inputs.fastq1.basename)
  46   - $(inputs.fastq2.basename)
  47
  48 s:codeRepository: https://github.com/arvados/arvados-tutorial/blog-examples/debugging
  49 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
  50
  51 $namespaces:
  52  s: https://schema.org/
  53  edam: http://edamontology.org/