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Update process-collect.nf #25

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meowcat
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@meowcat meowcat commented Oct 26, 2021

Fixes cases with a single file. Note that this example with cat would still work with a single file, but ls *.fq would not. nextflow-io/nextflow#2410

Fixes cases with a single file. Note that this example with `cat` would still work with a single file, but `ls *.fq` would not. nextflow-io/nextflow#2410
@pditommaso
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not understanding why ls *.fq is not working for a single file

@keiranmraine
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keiranmraine commented Apr 29, 2022

In the example if only a single input is passed the file is linked into the workspace as .fq, a hidden file as far as bash is concerned which is not available via *.fq.

Two issues:

  1. it would be preferable to always include the numeric, but I understand the possible implications of changing that.
  2. the example it should include a prefix so that hidden files aren't the default from the example:
process bar {
  echo true
  input:
  file 'in_*.fq' from unzipped_ch.collect()
  """
  cat in_*.fq
  """
}

@keiranmraine
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  1. file 'in_*.fq' from unzipped_ch.collect() a single file is file_.fq
  2. file 'in_?.fq' from unzipped_ch.collect() a single file is file_1.fq

(2) is certainly more consistent and obvious for the example

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3 participants