Question: CWL: glob patterns must not start with '/'
1
gravatar for sibyllewohlgemuth
3.5 years ago by
sibyllewohlgemuth20 wrote:

Hi,

I have problems getting the bwa-index.cwl to work: https://github.com/common-workflow-language/workflows/blob/master/tools/bwa-index.cwl

It only works when p is specified, otherwise I get an error "glob patterns must not start with '/' " because of the absolute path in the outputBinding (inputs.input.path). Does anyone have an idea how I can fix this without using the -p option?

Thanks a lot!

cwl • 995 views
ADD COMMENTlink modified 3.5 years ago by Michael R. Crusoe1.8k • written 3.5 years ago by sibyllewohlgemuth20
0
gravatar for Michael R. Crusoe
3.5 years ago by
Common Workflow Language project
Michael R. Crusoe1.8k wrote:

Hello sibyllewohlgemuth and thank you for asking this question.

The error was not yours. I've simplified and corrected the bwa index CWL description at https://github.com/common-workflow-language/workflows/pull/136 to fix the problem.

Cheers,

ADD COMMENTlink written 3.5 years ago by Michael R. Crusoe1.8k
1

Hi Micheal, Great, thanks a lot for fixing the file! Best, Sibylle

ADD REPLYlink written 3.5 years ago by sibyllewohlgemuth20
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