hi everyone, are there any plans to have multiqc natively support the

split_bam

module from RSeQC?

Does anyone know if Seqera is write in saying this > TSV Alternative: The TSV format is often more reliable and easier to work with for tables in MultiQC. I'm revisting trying to get the full parameter list listed in an (ideally) hidden list at teh bottom of teh table. I wanted to exploit this: https://github.com/nf-core/tools/blob/fee44dae3fb1f86561f8ee11a62eb6207804dc5d/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf#L73-L82 which produces

{
    "input": "<https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/samplesheet_reduced.csv>",
    "multiqc_config": null,
    "multiqc_title": null,
    "multiqc_logo": null,
    "max_multiqc_email_size": "25.MB",

To make a MultiQC compatible JSON as well (my idea was to just inject the MultiQC header info), but this appears to be MUCH more involved to modify the default nf-core parameter JSON to get it into the correct 'long' format of one column for parameter name and one for values than I had hoped... For example: If I just add the header section, like this

bash
{
  "id": "basic_pipeline_params",
  "section_name": "Basic Pipeline Parameters",
  "description": "Core configuration parameters",
  "plot_type": "table",
  "pconfig": {
    "id": "basic_params_table",
    "title": "Basic Configuration"
  },
  "data": {
    "input": "<https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/samplesheet_reduced.csv>",
    "outdir": "./results",
    "annotation_tool": "pyrodigal",
    "run_amp_screening": "true",
    "run_arg_screening": "true",
    "run_bgc_screening": "false"
  }
}

I get a long traceback error. To get it to work, I have to add an intermedia 'key' ( guess normally representing samples):

{
  "id": "pipeline_parameters",
  "section_name": "Pipeline Parameters",
  "description": "Configuration parameters used in the pipeline run",
  "plot_type": "table",
  "pconfig": {
    "id": "pipeline_params_table",
    "title": "Pipeline Configuration",
    "col1_header": "Parameter"
  },
  "data": {
    "Pipeline Configuration": {
      "input": "<https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/samplesheet_reduced.csv>",
      "multiqc_config": "null",
      "multiqc_title": "null",
      "multiqc_logo": "null",
      "max_multiqc_email_size": "25.MB",
      "multiqc_methods_description": "null"
    }
  }
}

But this is nasty because it ends up with a single row wide table with the sample name as 'Pipeline configuratio'n and each parameter is a column To make it wide table I have do this large structure change making each parameter it's own key...

{
  "id": "pipeline_parameters",
  "section_name": "Pipeline Parameters",
  "description": "Configuration parameters used in the pipeline run",
  "plot_type": "table",
  "pconfig": {
    "id": "pipeline_params_table",
    "title": "Pipeline Configuration"
  },
  "data": {
    "input": {
      "Value": "<https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/samplesheet_reduced.csv>"
    },
    "multiqc_config": {
      "Value": "null"
    },
    "multiqc_title": {
      "Value": "null"
    },
    "multiqc_logo": {
      "Value": "null"
    },
    "max_multiqc_email_size": {
      "Value": "25.MB"
    },

Seqera AI keeps telling me make it into a TSV table instead... (which indeed works straight out)

# id: 'pipeline_parameters'
# section_name: 'Pipeline Parameters'
# description: 'Configuration parameters used in the pipeline run'
# plot_type: 'table'
# pconfig:
#   id: 'pipeline_params_table'
#   title: 'Pipeline Configuration'
#   col1_header: 'Parameter'
Parameter	Value
input	<https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/samplesheet_reduced.csv>
multiqc_config	null
multiqc_title	null
multiqc_logo	null
max_multiqc_email_size	25.MB
multiqc_methods_description	null

*So: should I just drop the idea of using the JSON file and converting to TSV instead? *

Hello everyone, I am trying to get pbmarkdup log into MultiQC report. The search pattern of MultiQC is:

pbmarkdup:
  contents_re: LIBRARY +READS +UNIQUE MOLECULES +DUPLICATE READS
  num_lines: 5

I get this log, but it does not go into MultiQC report:

LIBRARY          READS    UNIQUE MOLECULES    DUPLICATE READS
----------   ----------  ------------------  -----------------
TRAC-2-8053       42511      42502 (100.0%)           9 (0.0%)
----------   ----------  ------------------  -----------------
TOTAL             42511      42502 (100.0%)           9 (0.0%)

We would like to distribute multiqc_report.html as-is but the Report generated on and Workflow Summary sections leak too much about our infrastructure: fusion mount points, bucket names, path prefixes, etc. Though clobbering these sections in the generated HTML works for now, I wonder if it might be possible to mask things ahead of time? Something like

--mask-path-prefix

/

--use-relative-paths-only

or similar?

Can we get a new release once this is merged? It is of the most importance

I am trying out the MultiQCSAV modules -> https://github.com/nf-core/modules/tree/master/modules/nf-core/multiqcsav as we want to use it in #C06PHJM0Y3D, using #C049MBCEW06 I capture all outputs from the pipeline. And I notice that while I still have all the files in the

multiqc_data/

folder, I am noticing no files at all in

multiqc_plots/pdf/

,

multiqc_plots/png/

and

multiqc_plots/svg/

. I am investigating, but just wanted to know if anyone noticed this

What's the recommended course of action for the new version of the multiqc tool in the module repository ? Do we wait for a template update or do we update it ourselves ?

Hello. Not sure if these should come here or on #CQY2U5QU9 Here’s a PR to add support for hifi_trimmer stats files in MultiQC: https://github.com/MultiQC/MultiQC/pull/3513

Hi all, when invoking multiqc in CI/CD , installed with micromamba, I get the following error:

Traceback (most recent call last):
    File "/root/CONDA/env-bf59e1c89e33c7658e72457bab39c109/bin/multiqc", line 6, in <module>
      from multiqc.__main__ import run_multiqc
    File "/root/CONDA/env-bf59e1c89e33c7658e72457bab39c109/lib/python3.14/site-packages/multiqc/__init__.py", line 25, in <module>
      from multiqc import (  # noqa: E402
      ...<2 lines>...
      )
    File "/root/CONDA/env-bf59e1c89e33c7658e72457bab39c109/lib/python3.14/site-packages/multiqc/config.py", line 25, in <module>
      from multiqc.utils.util_functions import strtobool, update_dict
    File "/root/CONDA/env-bf59e1c89e33c7658e72457bab39c109/lib/python3.14/site-packages/multiqc/utils/util_functions.py", line 14, in <module>
      import numpy as np
    File "/root/CONDA/env-bf59e1c89e33c7658e72457bab39c109/lib/python3.14/site-packages/numpy/__init__.py", line 112, in <module>
      from numpy.__config__ import show_config
    File "/root/CONDA/env-bf59e1c89e33c7658e72457bab39c109/lib/python3.14/site-packages/numpy/__config__.py", line 4, in <module>
      from numpy._core._multiarray_umath import (
      ...<3 lines>...
      )
    File "/root/CONDA/env-bf59e1c89e33c7658e72457bab39c109/lib/python3.14/site-packages/numpy/_core/__init__.py", line 24, in <module>
      from . import multiarray
    File "/root/CONDA/env-bf59e1c89e33c7658e72457bab39c109/lib/python3.14/site-packages/numpy/_core/multiarray.py", line 11, in <module>
      from . import _multiarray_umath, overrides
  RuntimeError: NumPy was built with baseline optimizations: 
  (X86_V2) but your machine doesn't support:
  (X86_V2).

Is there anything I can do about this ? installing another package ?

Maybe tricky, maybe not: Is there a semantic way to deal with per-sample tables in MultiQC? I have a structure like this

sample1.csv
gene,count
gene1,3
gene2,8

sample2.csv
gene,count
gene2,4
gene3,6

I would like to get a separate table for each sample, without mixing the data. The number and names of samples cannot be assumed. I have tried Seqera AI, but the solutions it suggests are somewhat convoluted (dynamic config generation).

I have a table that contains a lot of rows (up to tens of thousands). The table automatically gets converted to a violin plot. Is there any way to regain access to the table to allow the user to e.g. find the top samples by a column value? Obviously this can only work with table pagination, which I am not sure MultiQC supports.

Is it possible to export all the metrics collected by

multiqc

under

multiqc_data

folder as a JSON file?

Hi, about the issue with

rich.panel.Panel

https://github.com/MultiQC/MultiQC/issues/3536 Has the patch been pushed on conda? Thanks!

@Phil Ewels seeing an error on conda with Multiqc 1.33

>     File "/home/runner/tests/9ad412e6decd807638e570f612b7100a/work/conda/env-46cb47fa7c654ddf59f1c6f0e7915e5e/lib/python3.14/site-packages/multiqc/plots/plot.py", line 616, in initialize
    >       raise ValueError("No datasets to plot")
    >   ValueError: No datasets to plot
    >
    >   During handling of the above exception, another exception occurred:
    >
    >   Traceback (most recent call last):
    >     File "/home/runner/tests/9ad412e6decd807638e570f612b7100a/work/conda/env-46cb47fa7c654ddf59f1c6f0e7915e5e/bin/multiqc", line 10, in <module>
    >       sys.exit(run_multiqc())
    >                ~~~~~~~~~~~^^
    >     File "/home/runner/tests/9ad412e6decd807638e570f612b7100a/work/conda/env-46cb47fa7c654ddf59f1c6f0e7915e5e/lib/python3.14/site-packages/multiqc/__main__.py", line 21, in run_multiqc
    >       multiqc.run_cli(prog_name="multiqc")
    >       ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^
    >     File "/home/runner/tests/9ad412e6decd807638e570f612b7100a/work/conda/env-46cb47fa7c654ddf59f1c6f0e7915e5e/lib/python3.14/site-packages/click/core.py", line 1485, in __call__
    >       return self.main(*args, **kwargs)
    >              ~~~~~~~~~^^^^^^^^^^^^^^^^^
    >     File "/home/runner/tests/9ad412e6decd807638e570f612b7100a/work/conda/env-46cb47fa7c654ddf59f1c6f0e7915e5e/lib/python3.14/site-packages/rich_click/rich_command.py", line 216, in main
    >       rv = self.invoke(ctx)
    >     File "/home/runner/tests/9ad412e6decd807638e570f612b7100a/work/conda/env-46cb47fa7c654ddf59f1c6f0e7915e5e/lib/python3.14/site-packages/click/core.py", line 1269, in invoke
    >       return ctx.invoke(self.callback, **ctx.params)
    >              ~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    >     File "/home/runner/tests/9ad412e6decd807638e570f612b7100a/work/conda/env-46cb47fa7c654ddf59f1c6f0e7915e5e/lib/python3.14/site-packages/click/core.py", line 824, in invoke
    >       return callback(*args, **kwargs)
    >     File "/home/runner/tests/9ad412e6decd807638e570f612b7100a/work/conda/env-46cb47fa7c654ddf59f1c6f0e7915e5e/lib/python3.14/site-packages/multiqc/multiqc.py", line 545, in run_cli
    >       result = run(*analysis_dir, clean_up=clean_up, cfg=cfg, interactive=False)
    >     File "/home/runner/tests/9ad412e6decd807638e570f612b7100a/work/conda/env-46cb47fa7c654ddf59f1c6f0e7915e5e/lib/python3.14/site-packages/multiqc/multiqc.py", line 629, in run
    >       exec_modules(mod_dicts_in_order)
    >       ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^
    >     File "/home/runner/tests/9ad412e6decd807638e570f612b7100a/work/conda/env-46cb47fa7c654ddf59f1c6f0e7915e5e/lib/python3.14/site-packages/multiqc/core/exec_modules.py", line 157, in exec_modules
    >       rich.panel.Panel(
    >       ^^^^^^^^^^
    >   AttributeError: module 'rich' has no attribute 'panel'. Did you mean: 'pager'?

And seeing the same thing when I update to multiQC 1.34 with docker. Any idea?

Hi folks! I released MultiQC v1.35 last night, and a new thing that comes with it now is this MultiQC Configuration Wizard https://seqera.io/multiqc_config_wizard I think it could be quite nice for folks in nf-core: you can copy + paste your pipeline's MultiQC config into the editor and get it validated / explained, see if it's all needed (any default values) and then scroll through all of the available config values to see if there's anything you'd like to add. Let me know if you have any feedback!

Why is 1.35 not the latest?

At first, a thought that we have some samples with a strong 5' prime bias in our RNA-seq. But it turns out that my Firefox browser has a funny plot rendering bug that connects the first and last points with a straight line…. 😅

The latest multiqc seems to throw a

segfault

when using the linux docker image in compatibility mode on MacOS. I think this might have something to do (again) with the

polars

dependency, like we had in one of the previous versions.

@Phil Ewels is it OK to deprecate 'custom calculated' values from a module if it makes nonsense output? @Sofia Stamouli and I just identified that if you run FastQC on nanopore data, custom statistics the MultiQC module makes generates crazy values that do not correspond to anything Basically this line: https://github.com/MultiQC/MultiQC/blob/00d7f33df8cec2be307454119b2a8714e33a94f9/multiqc/modules/fastqc/fastqc.py#L417-L435 Where we think

# is within that range. Probably good enough though.

Actually is not good enough and is generating very misleading output 😅

Hi, sorry for the stupid question. Is there a way to force displaying all rows of a table? I have a table where the first column has duplicated values and it just displays the first occurrence of the unique values. EDIT: v 1.35

Fixing the links to the logos: https://github.com/MultiQC/logo/pull/2

Hi multiqc, I [posted recently] (https://nfcore.slack.com/archives/CE6SDBX2A/p1780970822992499) in #CE6SDBX2A but I think this latest error is distinct from the last one so I'm spinning up a new thread. Multiqc in the rnafusion pipeline gives me

memory allocation of 20 bytes failed

:

$ cat work/fc/505d1f97742a9359b2ad5b0e52d71e/.command.err
/// MultiQC 🔍 v1.33

            config | Loading config settings from: multiqc_config.yml
            config | Loading config settings from: multiqc.config.yml
     version_check | MultiQC Version v1.35 now available!
       file_search | Search path: /home/ochapman/test/nf-core-rnafusion/work/fc/505d1f97742a9359b2ad5b0e52d71e
       file_search | Module(s) in config.run_modules are unknown: arriba. Double check the case and dashes/underscores. Available modules IDs: adapterremoval, afterqc, anglerfish, ataqv, bakta, bamdst, bamtools, bases2fastq, bbduk, bbmap, bcftools, bcl2fastq, bclconvert, biobambam2, biobloomtools, biscuit, bismark, bowtie1, bowtie2, busco, bustools, ccs, cellranger, cellranger_arc, cells2stats, checkm, checkm2, checkqc, clipandmerge, clusterflow, conpair, custom_content, cutadapt, damageprofiler, dedup, deeptools, diamond, disambiguate, dragen, dragen_fastqc, eigenstratdatabasetools, fastp, fastq_screen, fastqc, featurecounts, fgbio, filtlong, flash, flexbar, freyja, ganon, gatk, gffcompare, glimpse, goleft_indexcov, gopeaks, gtdbtk, haplocheck, happy, hicexplorer, hicpro, hicup, hifiasm, hisat2, homer, hops, hostile, htseq, humid, interop, isoseq, ivar, jcvi, jellyfish, kaiju, kallisto, kat, kraken, leehom, librarian, lima, longranger, macs2, malt, mapdamage, megahit, metaphlan, methylqa, mgikit, minionqc, mirtop, mirtrace, mosaicatcher, mosdepth, motus, mtnucratio, multivcfanalyzer, nanoq, nanostat, nextclade, ngsbits, ngsderive, nonpareil, odgi, optitype, pairtools, pangolin, pbmarkdup, peddy, percolator, phantompeakqualtools, picard, porechop, preseq, prinseqplusplus, prokka, purple, pychopper, pycoqc, qc3C, qorts, qualimap, quast, ribotish, rna_seqc, rockhopper, rsem, rseqc, salmon, sambamba, samblaster, samtools, sargasso, seqera_cli, seqfu, seqkit, sequali, seqwho, seqyclean, sexdeterrmine, sickle, skewer, slamdunk, snippy, snpeff, snpsplit, somalier, sompy, sortmerna, sourmash, spaceranger, stacks, star, supernova, sylphtax, telseq, theta2, tophat, trimmomatic, truvari, umicollapse, umitools, varscan2, vcftools, vep, verifybamid, vg, whatshap, xengsort, xenium, xenome
       file_search | Only using modules: custom_content, picard, samtools, star, fastp, fastqc, fastqc

    custom_content | nf-core-rnafusion-methods-description: Found 1 sample (html)
    custom_content | nf-core-rnafusion-summary: Found 1 sample (html)
            picard | Found 1 InsertSizeMetrics reports
            picard | Found 1 MarkDuplicates reports
            picard | Found 1 RnaSeqMetrics reports
              star | Found 1 reports and 1 gene count files
             fastp | Found 1 reports
            fastqc | Found 4 reports
            fastqc | Found 2 reports
       file_search | Module(s) in config.run_modules are unknown: arriba. Double check the case and dashes/underscores. Available modules IDs: adapterremoval, afterqc, anglerfish, ataqv, bakta, bamdst, bamtools, bases2fastq, bbduk, bbmap, bcftools, bcl2fastq, bclconvert, biobambam2, biobloomtools, biscuit, bismark, bowtie1, bowtie2, busco, bustools, ccs, cellranger, cellranger_arc, cells2stats, checkm, checkm2, checkqc, clipandmerge, clusterflow, conpair, custom_content, cutadapt, damageprofiler, dedup, deeptools, diamond, disambiguate, dragen, dragen_fastqc, eigenstratdatabasetools, fastp, fastq_screen, fastqc, featurecounts, fgbio, filtlong, flash, flexbar, freyja, ganon, gatk, gffcompare, glimpse, goleft_indexcov, gopeaks, gtdbtk, haplocheck, happy, hicexplorer, hicpro, hicup, hifiasm, hisat2, homer, hops, hostile, htseq, humid, interop, isoseq, ivar, jcvi, jellyfish, kaiju, kallisto, kat, kraken, leehom, librarian, lima, longranger, macs2, malt, mapdamage, megahit, metaphlan, methylqa, mgikit, minionqc, mirtop, mirtrace, mosaicatcher, mosdepth, motus, mtnucratio, multivcfanalyzer, nanoq, nanostat, nextclade, ngsbits, ngsderive, nonpareil, odgi, optitype, pairtools, pangolin, pbmarkdup, peddy, percolator, phantompeakqualtools, picard, porechop, preseq, prinseqplusplus, prokka, purple, pychopper, pycoqc, qc3C, qorts, qualimap, quast, ribotish, rna_seqc, rockhopper, rsem, rseqc, salmon, sambamba, samblaster, samtools, sargasso, seqera_cli, seqfu, seqkit, sequali, seqwho, seqyclean, sexdeterrmine, sickle, skewer, slamdunk, snippy, snpeff, snpsplit, somalier, sompy, sortmerna, sourmash, spaceranger, stacks, star, supernova, sylphtax, telseq, theta2, tophat, trimmomatic, truvari, umicollapse, umitools, varscan2, vcftools, vep, verifybamid, vg, whatshap, xengsort, xenium, xenome
       file_search | Only using modules: picard, star, fastp, fastqc, fastqc, nf-core-rnafusion-methods-description, nf-core-rnafusion-summary

memory allocation of 20 bytes failed
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
memory allocation of 20 bytes failed
skipping backtrace printing to avoid potential recursion
/home/ochapman/test/nf-core-rnafusion/work/fc/505d1f97742a9359b2ad5b0e52d71e/.command.sh: line 11:    41 Aborted                 (core dumped) multiqc --force --config multiqc_config.yml --config multiqc.config.yml .

I tried disabling plotting based on other issues in this channel to no effect:

$ cat multiqc.config.yml
simple_output: true # same error toggling this flag as well
export_plots: false

Exit code is 134 and resources appear to be within limits for the job, suggesting that this seems to be an issue with Multiqc (or my configuration thereof) rather than purely a cluster or resource (mis)allocation issue. I'm now running rnaseq to see if it's reproducible from a different pipeline. Anyone seen this before? System information (UTokyo SHIROKANE): Nextflow: v26.04.3 Hardware: HPC Executor: AGE Container: configured as Singularity, but that's a symlink for Apptainer on this HPC OS: Red Hat Enterprise Linux 8.8 (x86_64) Runtime: Groovy 4.0.31 on OpenJDK 64-Bit Server VM 21.0.1+12-LTS Pipeline: nf-core/rnafusion 4.1.3

Hello! We have an external application that we are feeding information to by parsing the

multiqc_data.json

section

report_general_stats_data

. The issue we are having is that with the v1.29 release, general stats went from a list of dicts to a dict of dicts, crashing our parsing. To avoid this in the future, what is the recommended file to parse? Which is more stable? Or is multiqc_data.json still the right file to parse?

Hello 😊 I have attended to all (human and bot) reviewer comments in this PR: github.com/MultiQC/MultiQC/pull/3612 and submitted two separate PRs to fix mypy issues, separate from business logic: github.com/MultiQC/MultiQC/pull/3627 and github.com/MultiQC/MultiQC/pull/3613. 🙏🤓

Hello! Is the multiqc wizard down?

Adding MultiQC support to

mgnifam

subcommands. Test-data PR: github.com/MultiQC/test-data/pull/391 MultiQC PR: github.com/MultiQC/MultiQC/pull/3674

^one more reviewer for the second one (MultiQC PR) please? 😄 Tests green

Updating the MultiQC methurator module here: https://github.com/MultiQC/MultiQC/pull/3479 .The PR has been hanging around for a while, and since the module is now included in the dev branch of nf-core/methylseq, it would be great if we could get it finalized. Thanks!! 🙏 😬

I’m trying to add a subsection to the main Picard section using custom content. Is this possible? Current config:

namespace: picard
id: picard-crosscheckfingerprints-excluded-table
section_name: Samples excluded from fingerprinting
description: This table shows the samples excluded from fingerprinting due to insufficient
  coverage
plot_type: table
headers:
  sample: {}
  sites_sample: {}
  sites_snp: {}
  sites_overlap: {}
data:
  sample3: {sites_sample: 0, sites_snp: 9, sites_overlap: 0}

Hi, Is it possible to fitler the samples displayed in the General Statistics table in MultiQC? (still allowing all samples to be displaying normally inside modules) Thanks!