String editing for output file name

Question

[ttom]

This is a question related to String concatenation for output

This shell script outputs a file named R1_001_fastqc.results this is what I want to capture in the cwl. How could this be done ? The following code does not work

cat test.cwl

cwlVersion: v1.0
class: CommandLineTool
baseCommand: [sh, fastqc_check.sh]

requirements:
  - class: InlineJavascriptRequirement

inputs:
 fq1_zips:
  type: File
  inputBinding:
   position: 1

outputs:
 fastqc_check_out:
  type: File
  outputBinding:
   glob: $(inputs.fq1_zips.basename.split(".").slice(0)).results

cat test.yml

fq1_zips:
        class: File
        path: R1_001_fastqc.zip

fastqc_check_script:
 class: File
 path: fastqc_check.sh

[biokcb]

Does the answer I posted in the other post not do what you need? This seems like you want to do the same thing as that post, what is different about it?

[Kevin Blighe]

The user did indeed indicate that it worked: C: String concatenation for output

Can you clarify, ttom?

[ttom]

This time the output is R1_001_fastqc.results, I want to strip off the .zip from the output file. In the previous post the output was R1_001_fastqc.zip.results

The glob command below was tried to achieve the output filename as R1_001_fastqc.results

glob: $(inputs.fq1_zips.basename.split(".").slice(0)).results

Basically a part of the input file is used to name the outputfile name

Hope I am clear this time

Answer 1

[biokcb]

Oh, in that case use glob: $(inputs.fq1_zips.nameroot).results and remove the InlineJavascriptRequirement as it also isn't needed here.

edit to clarify: For future reference with File types nameroot refers to the filename without the extension and basename includes the extension.

[ttom]

Yes, it worked. Thanks !!

[drkennetz]

You should mark it as accepted if it answered your question.

Answer 2

[ttom]

What if the output file should be named SampleA_fastqc.summary according to the inputs/sample as shown below

cat test.cwl cwlVersion: v1.0 class: CommandLineTool baseCommand: [sh, fastqc_check.sh]

inputs:
 sample:
  type: string
  inputBinding:
   position: 1
 fq1_zips:
  type: File
  inputBinding:
   position: 2

outputs:
 fastqc_check_out:
  type: File
  outputBinding:
   glob: $(inputs.sample.basename)_fastqc.summary

cat test.yml

sample: SampleA
fq1_zips:
        class: File
        path: R1_001_fastqc.zip

fastqc_check_script:
 class: File
 path: fastqc_check.sh

[biokcb]

Since sample is a string type, you don't need basename, as that is a File type attribute. Just use glob: $(inputs.sample)_fastqc.summary

[ttom]

This works...Thank you