CWLtools version problem with usage of secondary files and java expression

Question

[a.james]

Dear All,

I have tried using java expression to capture all secondary files from STAR aligner in CWLtools version from 2018 October and 2019 February.

On 2018 October version it is running successfully without any issues, whereas on 2019 February version it is throwing error.

Here is what I tried : the last part where I added secondary files on star.cwl, ignores to capture the log files.

secondaryFiles: |
    ${
         var p=inputs.outFileNamePrefix?inputs.outFileNamePrefix:"";
         return [
           {"path": p+"Log.final.out", "class":"File"},
           {"path": p+"SJ.out.tab", "class":"File"},
           {"path": p+"Log.out", "class":"File"}
         ];
     }

And on 2019 February version the same tool is throwing following error,

May 03 19:09:00 ..... started STAR run
May 03 19:09:00 ..... loading genome
May 03 19:09:19 ..... started mapping
May 03 19:09:50 ..... started sorting BAM
May 03 19:09:52 ..... finished successfully
[job star] Max memory used: 1461MiB
[job star] Job error:
Error collecting output for parameter 'star_bam':
cwltools/star.cwl:182:3: string indices must be integers
[job star] completed permanentFail

Any suggestions help is much appreciated!! Thank you

[a.james]

I solved the issue . https://github.com/common-workflow-language/cwltool/issues/1110

Answer 1

[a.james]

I solved the issue . https://github.com/common-workflow-language/cwltool/issues/1110