requirements:
DockerRequirement:
- dockerPull: curii/fastqc
- InitialWorkDirRequirement:
- listing:
- - $(inputs.fastq1)
- - $(inputs.fastq2)
+ dockerPull: biocontainers/fastqc:v0.11.9_cv6
hints:
SoftwareRequirement:
version: [ "0.11.9" ]
inputs:
- fastq1:
+ fastq1:
type: File
format: edam:format_1930 # FASTQ
label: One of set of pair-end FASTQs (R1)
- fastq2:
+ fastq2:
type: File
format: edam:format_1930 # FASTQ
label: One of set of pair-end FASTQs (R2)
out-html:
type: File[]
label: FASTQ QC reports
- format: edam:format_1964 # HTML
+ format: edam:format_2331 # HTML
outputBinding:
glob: "*html"
out-zip:
outputBinding:
glob: "*fastqc.zip"
-baseCommand: perl
+baseCommand: fastqc
arguments:
- - /FastQC/fastqc
- - $(inputs.fastq1.basename)
- - $(inputs.fastq2.basename)
+ - $(inputs.fastq1.path)
+ - $(inputs.fastq2.path)
s:codeRepository: https://github.com/arvados/arvados-tutorial
s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
s: https://schema.org/
edam: http://edamontology.org/
-$schemas:
- - https://schema.org/version/latest/schema.rdf
- - http://edamontology.org/EDAM_1.18.owl
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl