hard copies instead of symlinks from InitialWorkDirRequirement ? - SOLVED

Question

[jeltje.van.baren]

NOTE: The below was due to using an older version of cwl-runner.

I am trying to debug https://github.com/Sage-Bionetworks/SMC-RNA-Examples/blob/master/workflow/smcFusionQuant-INTEGRATE-workflow.cwl One of the issues is that I can't figure out how to get the input and output of a tool in the same location so that I can pass them to the next step in the workflow.

Details: As part of this workflow, I am trying to run samtools index on bam files created earlier in the pipeline.

requirements:
  - class: InlineJavascriptRequirement
  - class: InitialWorkDirRequirement
    listing:
      - $(inputs.bam)

What this creates though is a symlink to the local docker container:

lrwxrwxrwx  1 ubuntu ubuntu   65 Dec  6 09:55 unmapped.bam -> /var/lib/cwl/stg80eb5f7c-d51f-4ca0-898d-175a1c487761/unmapped.bam
-rw-r--r--  1 ubuntu root    216 Dec  6 09:55 unmapped.bam.bai

The next program in the workflow looks for a bam file and assumes a bam.bai file. And of course the link is now broken, so the workflow crashes with

  Missing input file [Errno 2] No such file or directory: '/mnt/integrate/tempdir7Np3TT/unmapped.bam

How do I create a workflow so that the bam and the bam.bai file end up in the same spot?

[maitai]

How did you solve this problem?

[jeltje.van.baren]

I was using an older version of cwl. Once I upgraded, the problem went away.

One thing I couldn't figure out for a while is how to call initialWorkDir properly. Here's the relevant piece of cwl:

requirements:
  - class: InlineJavascriptRequirement
  - class: InitialWorkDirRequirement
    listing:
      - $(inputs.src)

inputs:
  src:
    type: File
    inputBinding:
      position: 1
      valueFrom: $(self.basename)

Note the $(self.basename) For some reason this is necessary to make the requirements section understand which file to stage.