8000 [nonpareil] Add missing anchors by fgvieira · Pull Request #3429 · MultiQC/MultiQC · GitHub
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[nonpareil] Add missing anchors #3429

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[nonpareil] Add missing anchors #3429

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@fgvieira fgvieira commented Dec 9, 2025

Add anchor on id, so it is possible to change it from config.

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

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ewels commented Dec 9, 2025

Can you explain a bit more what the problem is that you're solving here please?

@fgvieira fgvieira changed the title [samtools] Add missing anchors [nonpareil] Add missing anchors Dec 10, 2025
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fgvieira commented Dec 10, 2025

Sorry for the short description, but you were too fast! Here goes a more thorough explanation. 😄

Multiple plots

The immediate idea, was to allow nonpareil (and initially samtools) to have custom plot ids, so that there can be several plots in the same report with meaningful IDs. I think the general problem (as already hinted at in #2203,#2206, #2076, MultiQC/MegaQC#484) is that section anchors and plot ids are not standardized:

  • some are hard-coded, while others use the anchor in the plot ID
  • no specific naming structure (so some plots end up with id="fastqc_sequence_counts_sequence_counts_plot")

In the nonpareil module the ids were hard-coded, so I added the anchor to the id and tried to standardized it a bit:

  • anchor: module name and type of data in the section (e.g. "stats"," saturation", "adapter content"), separated by (e.g.) "-".
  • plot id: anchor and how the data is shown/plotted (e.g. "table", "plot", "barplot"), separated by (e.g.) "_"

This way, if the user specifies a new anchor (e.g. "nonpareil-longread"), the plot id is still meaningful ("nonpareil-longread_plot").

JSON

On the other hand, if the idea is to use self.anchor as a prefix to the plot ids (which I think it should!), then I'd say it would also make sense to use the same prefix when writing the data file. Right now the module specifies its own prefix (e.g. on "fastqc"):

  • if anchor defined as "raw-fastqc" in config
  • plot id for the sequence count becomes "raw-fastqc_sequence_counts_plot"
  • raw data on json file is stored as "multiqc_fastqc_raw-fastqc", because of self.write_data_file(dump_data, "multiqc_fastqc")

General Suggestion

As a general suggestion, I'd say that both anchor, ids and json keys should be auto-generated by multiqc internally, and that the only variable would be a prefix. By default, this would be the module name but it could be overwritten by the user (e.g. in the config).
As for the auto-generated IDs, I'd suggest something like:

  • plots
    • anchor would be {prefix}_datatype
    • ids would be {anchor}_plottype.
    • So, for (e.g.) fastqc sequence counts barplot, it would be:
      • prefix = "fastqc"
      • anchor = "{prefix}_sequence_counts"
      • id = "{anchor}_bargraph"
      • This would lead to id = "fastqc_sequence_counts_bargraph" (instead of current "fastqc_sequence_counts_sequence_counts_plot")
  • json keys, instead of multiqc_textdefniedbymodule_{anchor}, would be only multiqc_{anchor}

Hope it now makes more sense! 😄

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@fgvieira @ewels
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