This is a test version of Biostars. For the public version, visit https://www.biostars.org.
CWL : output file refer to inputs param

I mean refer some filed from input params For exampe: input param contains this field：
prefix： * output file ,i want the [prefix].fq.gz ,but not the [prefix].stat so ,can i write the cwl by glob: $(inputs.extractfile).fq.gz ?

cwl
• 1,698 views • link
written by lizhichao lizhichao

2 answers

ok,so,i can refer to the more specific fields.Thank you very much !

• 0 views • link
written by lizhichao lizhichao

emm，i tested，its ok.

cwlVersion: v1.0 class: CommandLineTool baseCommand: [tar, --extract] inputs: tarfile: type: File inputBinding: prefix: --file extractfile: type: string inputBinding: position: 1 prefix: type: string outputs: extracted_file: type: File outputBinding: glob: $(inputs.prefix).txt

• 0 views • link
written by lizhichao lizhichao

This will work for string inputs. I'm adding this in case somebody reading has to handle files. Let's say our input file is named "aspergillus.fastq".

The inputs section is:

inputs:
  reads:
    type: File
    inputBinding:
      prefix: -r

Referencing the input:

$(inputs.reads.basename) = "aspergillus.fastq"

$(inputs.reads.nameroot) = "aspergillus"

$(inputs.reads.nameext) = ".fastq"

• 0 views • link
written by Tom Tom

Log in to answer this question.

More posts like this