CWL Workflow renaming outputs

[Ryan Golhar]

Hi all - I'm getting up to speed on CWL and am running into some questions/issues.  I know biostars is the place to go to but I see some of my questions have similar ones that are unanswered.  For example, I have a similar situation to https://www.biostars.org/p/325829/.   If my tool has something like:

outputs:

  std_out:

    type: stdout

stdout: stdout.txt

and my workflow has:

steps:

  fastQValidator1:

    run: Dockerfiles/fastQValidator/fastQValidator.cwl

    in:

      fastq_file: fastq1

    out: [std_out]

  fastQValidator2:

    run: Dockerfiles/fastQValidator/fastQValidator.cwl

    in:

      fastq_file: fastq2

    out: [std_out]

outputs:

  fqValidator1_out:

    type: File

    outputSource: fastQValidator1/std_out

  fqValidator2_out:

    type: File

    outputSource: fastQValidator2/std_out

How would I rename std_out from my workflow, instead of the tool?  I want to leave the tool generic and customize the outputs using the workflow.

[Michael Crusoe]

Hello Ryan,

Sorry for the very late reply!

If you can't customize the output file from within the CommandLineTool based upon aspects of the inputs then consider a standalone CWL `ExpresionTool` to do the renaming. An extreme version that renames a collections of files and folders is at https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl/blob/master/workflows/convert-to-v3-layout.cwl

For others, https://www.commonwl.org/user_guide/misc/#rename-an-output-file may also be interesting.

--
You received this message because you are subscribed to the Google Groups "common-workflow-language" group.
To unsubscribe from this group and stop receiving emails from it, send an email to common-workflow-la...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/common-workflow-language/86771130-2d1d-483c-af7f-353ebdb60127%40googlegroups.com.

--

Michael R. Crusoe
Co-founder & Lead,
Common Workflow Language project
https://orcid.org/0000-0002-2961-9670
m...@commonwl.org