tabix and CWL

Question

[thomas.e]

I'm trying to incorporate tabix into a workflow and I'm getting:

[job gridss-tabix] /stornext/HPCScratch/home/thomas.e/tmp/tmpdR3yDK$ tabix \
    --preset \
    vcf \
    /stornext/HPCScratch/home/thomas.e/tmp/tmp5etQrA/stg4113c1c5-9ba1-49ff-a6de-d9444c432acc/S1_R1.trimmed.sorted.human.gridss.vcf.gz
[job gridss-tabix] Job error:
../tools/src/tools/tabix.cwl:141:3: Error collecting output for parameter 'tabix':
../tools/src/tools/tabix.cwl:144:7:   Did not find output file with glob pattern: '['S1_R1.trimmed.sorted.human.gridss.vcf.gz.tbi']'

I seem to be benefiting from CWL not wanting to access files in the input directory.

https://github.com/common-workflow-language/common-workflow-language/issues/280

What is the solution here?

Answer 1

[thomas.e]

I was able to solve the problem by requiring the input file to be in the work directory in my tool

requirements:
- class: InitialWorkDirRequirement
  listing: [ $(inputs.inputFile) ]