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use nf-core framework for CLI help and log messages #33

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4 tasks done
fmalmeida opened this issue Feb 22, 2022 · 3 comments
Closed
4 tasks done

use nf-core framework for CLI help and log messages #33

fmalmeida opened this issue Feb 22, 2022 · 3 comments

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@fmalmeida
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fmalmeida commented Feb 22, 2022 •
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Change the pipeline configurations a little bit to:

  • Better reorganize the config files, updating standard to do not load any other profile as is common for NF pipelines
  • Better separate defaults params from the main config and script
  • Use label resources to better manage parallel jobs as it is done by nf-core
  • Use more of nf-core framework and Groovy libs to provide beautiful and cleaner CLI help and log messages
@fmalmeida fmalmeida changed the title us nf-core framework for CLI help and log messages use nf-core framework for CLI help and log messages Feb 22, 2022
@fmalmeida
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Implementation going on in dev branch

@fmalmeida
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Seems properly implemented. Must now check documentation to identify snippets that need to be updated.

@fmalmeida fmalmeida mentioned this issue Feb 28, 2022
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@fmalmeida
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It has been added.

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