Replace-names

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1

In my MultiQC reports, the sample names have several different patterns due to different analyses. The patterns include barcodeXX, barcodeXX.reor_consensus, and barcodeXX.reor_consensus.fasta. I would like to use --replace-names to get rid of the suffixes, so I added the following code to my config file:

sample_names_replace_regex: true

sample_names_replace:

  "barcode(\\d{2})\\.reor_consensus(\\.fasta)?": "barcode\\1"

However, it did not remove the suffixes as expected. I need help, Thanks

2

If it’s just suffixes, you don’t want to replace the names - you want to clean them.

In your case, your config should look something like this:

extra_fn_clean_exts:
  - ".reor_consensus"

That’ll match .reor_consensus anywhere in a sample name and remove it - and anything after it (including the .fasta).

Hope that helps!

Phil

3

Dear ewels

Thank you for the reply, but it didn’t work for me.

I have tried

extra_fn_clean_exts:

  - ".reor_consensus"

and/or

extra_fn_clean_trim:

  - ".reor_consensus"

including the --replace-names, but nothing works.

From multiqc --verbose

it does register the pattern specified in the config, but somehow it doesn’t do the job as expected.

[2026-01-12 00:29:10] multiqc.config                                     [DEBUG  ]  Added to filename clean extensions: [['.reor_consensus']]
[2026-01-12 00:29:10] multiqc.config                                     [DEBUG  ]  Added to filename clean trimmings: [['.reor_consensus']]

here is one example, the CheckM2 report didn’t clean the file name: the name ends with .reor_consensus, but even with the extra_fn_clean_exts: in the config, it still doesn’t cleanup the suffix.

[2026-01-12 00:29:34] multiqc.core.exec_modules                          [DEBUG  ]  Running module: checkm2
[2026-01-12 00:29:34] multiqc.modules.checkm2.checkm2                    [INFO   ]  Found 16 reports
[2026-01-12 00:29:34] multiqc.report                                     [DEBUG  ]  Wrote data file multiqc_checkm2.txt
[2026-01-12 00:29:34] multiqc.report                                     [DEBUG  ]  Wrote data file multiqc_checkm2.json
[2026-01-12 00:29:34] multiqc.plots.table_object                         [DEBUG  ]  Table key 'Additional_Notes' not found in data for 'checkm2-first-table'. Skipping. Check for possible typos between data keys and header keys
[2026-01-12 00:29:34] multiqc.plots.plot                                 [DEBUG  ]  merge_with_previous for checkm2-first-table: found old_data = False
[2026-01-12 00:29:34] multiqc.plots.plot                                 [DEBUG  ]  merge_with_previous for checkm2-first-table: no old data or empty, using new data only
[2026-01-12 00:29:34] multiqc.core.software_versions                     [DEBUG  ]  Reading software versions from config.software_versions
[2026-01-12 00:29:34] multiqc.core.software_versions                     [DEBUG  ]  Reading software versions settings from: pipeline_info/bacteria_mqc_versions.yaml

By the way, the multiqc version is V1.33

4

Ah, you’re not doing anything wrong. It looks like these modules are incorrectly not using the self.clean_s_name() function from MultiQC which does this sample name cleaning.

I’ve just opened a PR to address this:

Once that is merged and released, it should work. You can try installing from this dev branch to test locally in the mean time:

pip install git+https://github.com/MultiQC/MultiQC.git@musing-beaver

Thanks for checking, hopefully this should do the job. Let me know how you get on!

5

Thank you ewels, One more thing, would this fix also apply to custom contents?

6

Custom content should already be correctly applying the sample name cleaning, so that should already work :+1:

7

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