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Channel operations toList followed by merge hang #1083

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glormph opened this issue Mar 20, 2019 · 3 comments
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Channel operations toList followed by merge hang #1083

glormph opened this issue Mar 20, 2019 · 3 comments
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@glormph
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glormph commented Mar 20, 2019

Bug report

Expected behavior and actual behavior

Converting a channel to a list with toList, followed by merge to another channel works as expected (it merges the channels), but actual behaviour is that this happens, but the pipeline hangs after all the steps have been processed. Not sure if I'm doing it wrong here.

Steps to reproduce the problem

q1 = Channel.from([0, 'a'])

process test {
  output:
  file('hello') into q2

  """
  touch hello
  """
}

q1
  .toList()  // replacing with .buffer(size: 2) works fine.
  .merge(q2)
  .println{it}

Program output

$ nextflow run  small_tolist.nf
N E X T F L O W  ~  version 18.10.1
Launching `/Z/jorrit/repos/testnfcddadeq/small_tolist.nf` [awesome_murdock
[nextflow.log](https://github.com/nextflow-io/nextflow/files/2987949/nextflow.log)
] - revision: 690b801a5c
[warm up] executor > local
[15/261c24] Submitted process > test
[0, a, /path/to/nfrepo/work/15/261c24a59553470addc29f88b57e5e/hello]

... minutes pass ...

^C
$ 

Environment

  • Nextflow version: [18.10.1, 19.01.0.5050]
  • Java version: [11]
  • Operating system: [Ubuntu 18.04]

Additional context

@glormph
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glormph commented Mar 20, 2019

If it's at all interesting, I can add that using collect instead of toList results in the same behaviour.

@pditommaso pditommaso added the bug label Mar 27, 2019
@pditommaso pditommaso added this to the v19.04.0 milestone Mar 27, 2019
@pditommaso
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Found the problem, thanks for reporting it.

@pditommaso pditommaso changed the title Channel operations toList followed by merge work, but blocks completion? Channel operations toList followed by merge hang Mar 27, 2019
@glormph
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glormph commented Mar 28, 2019

Thank you very much for fixing! :) 👍

glormph added a commit to glormph/nf-core-dda-quant-proteomics that referenced this issue May 2, 2019
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