blog-examples/debugging/fastq_example/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
   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     label: One of set of pair-end FASTQs (R1)
  20   fastq2:
  21     type: File
  22     label: One of set of pair-end FASTQs (R2)
  23
  24 outputs:
  25   out-html:
  26     type: File[]
  27     label: FASTQ QC reports
  28     outputBinding:
  29       glob: "*html"
  30   out-zip:
  31     type: File[]
  32     label: Zip files of FASTQ QC report and associated data
  33     outputBinding:
  34       glob: "*fastqc.zip"
  35
  36 baseCommand: fastqc
  37
  38 arguments:
  39   - "--noextract"
  40   - $(inputs.fastq1.path)
  41   - $(inputs.fastq2.path)
  42
  43 s:codeRepository: https://github.com/arvados/arvados-tutorial/blog-examples/debugging
  44 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
  45
  46 $namespaces:
  47  s: https://schema.org/
  48  edam: http://edamontology.org/