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docs: describe workflow rationale #135

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@deliaBlue deliaBlue commented Jan 31, 2024

This PR closes #126.

The changes applied are:

  • Correct file extensions, typos, explanations and add examples in some rules in the pipeline_documentation.md
  • Expand the workflow description and fix typos in the main README.

@deliaBlue deliaBlue added the documentation Improvements or additions to documentation label Jan 31, 2024
@deliaBlue deliaBlue self-assigned this Jan 31, 2024
@deliaBlue deliaBlue linked an issue Jan 31, 2024 that may be closed by this pull request
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@uniqueg uniqueg left a comment

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Couple of issues, but shouldn't take long to fix. Didn't look at all of the many changes in the pipeline documentation file carefully - but it looks mostly fine :)

To be fair, it's probably one of the 10 most detailed pipeline documentations ever written 🤣

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Comment on lines +774 to +777
> Given the short length of the reads, the sequence similarity among miRNAs,
> and the merging of two different mapping results, the number of hits can
> be notably high. Therefore, reads aligned beyond a specified value are
> disregarded.
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Same comment as in the other file applies.

Comment on lines +753 to +756
> Given the short length of the reads, the sequence similarity among miRNAs,
> and the merging of two different mapping results, the number of hits can
> be notably high. Therefore, reads aligned beyond a specified value are
> disregarded.
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Same comment as in the other file applies.

Comment on lines +703 to +705
> Given the short length of the reads and the sequence similarity among miRNAs,
> the number of hits can be notably high. Therefore, reads aligned beyond a
> specified value are disregarded.
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Same comment as in the other file applies.

Comment on lines +651 to +653
> Given the short length of the reads and the sequence similarity among miRNAs,
> the number of hits can be notably high. Therefore, reads aligned beyond a
> specified value are disregarded.
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Same comment as in the other file applies.

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uniqueg commented Mar 18, 2024

Oh, and please check why the static code analysis fails.

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Please address the open comments and send for re-review when you are done 🙏

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docs: describe workflow rationale
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