8000 Unclear points in documentation · Issue #267 · nf-core/taxprofiler · GitHub
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Unclear points in documentation #267

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prototaxites opened this issue Mar 14, 2023 · 1 comment · Fixed by #271
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Unclear points in documentation #267

prototaxites opened this issue Mar 14, 2023 · 1 comment · Fixed by #271
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bug Something isn't working documentation Improvements or additions to documentation
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1.1.0 - Augmented...

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@prototaxites
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prototaxites commented Mar 14, 2023 •
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Description of the bug

Hi all, a couple of points for the documentation that need clarifying:

  1. In the additional help dropdown on the params page, the text for, --run_profile_standardisation states “This currently only is generated for mOTUs.“, but enabling this option turns on standardisation for all profilers.

  2. The Multi-Table Generation section of the usage guide does not supply the required parameter (--run_profile_standardisation) in order to enable consolidation of profiling reports.

  3. The tutorial section on installing/downloading the mOTUs database should make clear that the name of the mOTUs database directory should not be changed (from db_mOTU) if it is moved from the install location. I initially renamed the directory when moving it to a centralised location and mOTUs refused to run as the directory name is hard-coded.

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@prototaxites prototaxites added bug Something isn't working documentation Improvements or additions to documentation and removed bug Something isn't working labels Mar 14, 2023
@jfy133 jfy133 self-assigned this Mar 14, 2023
@jfy133 jfy133 added this to the 1.1.0 - Augmented Akita milestone Mar 14, 2023
@jfy133 jfy133 added the bug Something isn't working label Mar 14, 2023
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jfy133 commented Mar 17, 2023 •
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  • In the additional help dropdown on the params page, the text for, --run_profile_standardisation states “This currently only is generated for mOTUs.“, but enabling this option turns on standardisation for all profilers.
  • The Multi-Table Generation section of the usage guide does not supply the required parameter (--run_profile_standardisation) in order to enable consolidation of profiling reports.
  • The tutorial section on installing/downloading the mOTUs database should make clear that the name of the mOTUs database directory should not be changed (from db_mOTU) if it is moved from the install location. I initially renamed the directory when moving it to a centralised location and mOTUs refused to run as the directory name is hard-coded.

@jfy133 jfy133 mentioned this issue Mar 17, 2023
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@jfy133 jfy133 linked a pull request Mar 17, 2023 that will close this issue
Standardised taxon table and mOTU database docs improvement #271
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@jfy133 jfy133 closed this as completed Mar 22, 2023
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Standardised taxon table and mOTU database docs improvement nf-core/taxprofiler
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