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cwl glob all the output files in a directory

iI try to capture all the output files in the directory 【./fpfn】by glob ./fpfn/* . But It failed, the error is :Error validating output record. theoutputfield is not valid \n because item is invalid \n because Expected class 'File' but this is 'Directory' So my grammar wrong? and How can I capture all the files in a directory? Thanks !

cwl
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updated by Michael R. Crusoe Michael R. Crusoe • written by lizhichao lizhichao

1 answer

Hello lizhichao,

Sounds like one of the items in your directory is another directory.

You can work around that by either adjusting your glob to be more specific, or adjusting your type specification.

I'm guessing that currently you have type: File[] or similar right now. If you can't restrict the glob further then try the following:

outputs:
   my_output:
      type:
        type: array
        items: [ File, Directory ]
      outputBinding:
        glob:  ./fpfn/*
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written by Michael R. Crusoe Michael R. Crusoe

In fact，when I try to be more specific ，It worked. In addition ,I will try the writting format:items: [ File, Directory ] Thank you!

• 0 views • link
written by lizhichao lizhichao

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