Question: CWL Workflow removing input files
0
gravatar for Tom
7 months ago by
Tom430
Bielefeld University, CeBiTec, Germany
Tom430 wrote:

I want use deepbinner as the first step of a workflow. Deepbinner scans fast5 files for barcodes and then moves them to different folders accordingly. My problem is that files are sorted into a temp directory created by cwltool and disappear from their original location. The temporary files are then processed further and i get my desired output. However, all my raw data is lost.

Is there a way to prevent this behavior? I would like for the workflow to not alter the input directory at all, but i don't know how to make sure deepbinner only gets a copy of the directory.

cwl deepbinner • 315 views
ADD COMMENTlink modified 6 months ago • written 7 months ago by Tom430
1

Hello Tom,

Which CWL runner are you using, and which version is it?

Do your CWL descriptions use the DockerRequirement?

Can you share a link to view your CWL descriptions?

ADD REPLYlink written 7 months ago by Michael R. Crusoe1.6k

I'm using cwltool version is 1.0.20181217162649 I am still struggling with getting my stuff to work with docker, so for now there is no DockerRequirement.

I added the relevant code to a repository: *edit: repository made private again.

Thank you for taking the time to help.

ADD REPLYlink modified 6 months ago • written 7 months ago by Tom430
1

In case it is of interest: When running the tool in Docker it fails because it cannot move the input files out of their directories.

Using InitialWorkDirRequirement with writable: true solves the problem.

ADD REPLYlink written 6 months ago by Tom430
1
gravatar for Tom
6 months ago by
Tom430
Bielefeld University, CeBiTec, Germany
Tom430 wrote:

Using InitialWorkDirRequirement with a writable: field set to true solves the problem. CWLtool seems to copy all files into a temporary directory and deepbinner is then able to move them out of there.

requirements:
  InlineJavascriptRequirement: {}
  InitialWorkDirRequirement:
    listing:
      - entry: $(inputs.reads_directory)
        writable: true
ADD COMMENTlink modified 6 months ago • written 6 months ago by Tom430
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