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Add samtools ampliconclip stats support#3214

Merged
vladsavelyev merged 7 commits into
MultiQC:mainfrom
nh13:feat/samtools-ampliconclip
Jun 7, 2025
Merged

Add samtools ampliconclip stats support#3214
vladsavelyev merged 7 commits into
MultiQC:mainfrom
nh13:feat/samtools-ampliconclip

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@nh13

@nh13 nh13 commented May 31, 2025

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  • This comment contains a description of changes (with reason)

Adding support for the stats file from samtools ampliconclip.

  • There is example tool output for tools in the https://github.com/MultiQC/test-data repository or attached to this PR
    See: Add samtools ampliconclip stats test data test-data#347
  • Code is tested and works locally (including with --strict flag)
  • Everything that can be represented with a plot instead of a table is a plot
  • Report sections have a description and help text (with self.add_section)
  • There aren't any huge tables with > 6 columns (explain reasoning if so)
  • Each table column has a different colour scale to its neighbour, which relates to the data (e.g. if high numbers are bad, they're red)
  • Module does not do any significant computational work

Comment thread multiqc/core/special_case_modules/custom_content.py Outdated
@nh13

nh13 commented Jun 5, 2025

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@ewels any chance you could take a look at this?

@vladsavelyev vladsavelyev added this to the v1.30 milestone Jun 6, 2025
@vladsavelyev

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Thank you! A few updates to fix linting, and looks good

@vladsavelyev vladsavelyev self-requested a review June 6, 2025 15:36
Comment thread multiqc/modules/samtools/ampliconclip.py Outdated
@nh13

nh13 commented Jun 7, 2025

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@vladsavelyev can you merge? I don't have permission...

@vladsavelyev vladsavelyev merged commit 9e985ee into MultiQC:main Jun 7, 2025
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@vladsavelyev

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@nh13 Merged! Thanks a lot for the addition :)

@nh13 nh13 deleted the feat/samtools-ampliconclip branch June 7, 2025 14:21
@nh13

nh13 commented Jun 7, 2025

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Thank you for the review!

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2 participants