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.
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?