+++ /dev/null
-cwlVersion: v1.1
-class: CommandLineTool
-label: Quality check on FASTQ
-
-requirements:
- DockerRequirement:
- dockerPull: biocontainers/fastqc:v0.11.9_cv6
- InitialWorkDirRequirement:
- listing:
- - $(inputs.fastq1)
- - $(inputs.fastq2)
-
-hints:
- SoftwareRequirement:
- packages:
- FastQC:
- specs: [ "https://identifiers.org/rrid/RRID:SCR_014583" ]
- version: [ "0.11.9" ]
-
-inputs:
- fastq1:
- type: File
- label: One of set of pair-end FASTQs (R1)
-
- fastq2:
- type: File
- label: One of set of pair-end FASTQs (R2)
-
-outputs:
- out-html:
- type: File[]
- label: FASTQ QC reports
- outputBinding:
- glob: "*html"
- out-zip:
- type: File[]
- label: Zip files of FASTQ QC report and associated data
- outputBinding:
- glob: "*fastqc.zip"
-
-baseCommand: fastqc
-
-arguments:
- - "--noextract"
- - $(inputs.fastq1.basename)
- - $(inputs.fastq2.basename)
-
-s:codeRepository: https://github.com/arvados/arvados-tutorial/blog-examples/debugging
-s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
-
-$namespaces:
- s: https://schema.org/
- edam: http://edamontology.org/