Multiple FASTQC module sections are combined

[Lfulcrum]

Description of bug

System info

• macOS Sonoma - Version 14.5 (23F79)
• multiQC v1.22.1

Opened report with multiple browsers (same symptoms):

• Firefox 126.0
• Chrome Version 125.0.6422.77 (Official Build) (x86_64)

Symptoms
When creating a report with two sections for the FASTQC module (e.g. one section for raw fastq data, another for trimmed), the second section is ignored. Or rather the stats of the second section overwrite the stats for the first section, such that the second section report appears combined with the metadata (e.g. section name) of the first section. Hopefully easier to see with the report provided 🤞

There are no error messages on the report or in the Developer Tools console.

File that triggers the error

multiQC report
multiqc_report.html.gz

multiQC minimal config
multiqc_config.yml.gz

MultiQC Error log

$ multiqc -n multiqc_report.html -f --config ../config/multiqc/multiqc_config.yml -v .

/// MultiQC 🔍 v1.22.1

[2024-05-23 10:34:23] multiqc.core.update_config                         [DEBUG  ]  This is MultiQC v1.22.1
[2024-05-23 10:34:23] multiqc.core.update_config                         [DEBUG  ]  Running Python 3.11.6 (main, Nov 16 2023, 10:12:38) [GCC 13.1.0]
[2024-05-23 10:34:23] multiqc.config                                     [INFO   ]  Loading config settings from: ../config/multiqc/multiqc_config.yml
[2024-05-23 10:34:23] multiqc.config                                     [DEBUG  ]  New config: {'run_modules': ['fastqc'], 'module_order': [{'fastqc': {'name': 'FastQC: raw', 'path_filters_exclude': ['fastqc/raw/*']}}, {'fastqc': {'name': 'FastQC: trimmed', 'path_filters': ['fastqc/trim/*']}}]}
[2024-05-23 10:34:23] urllib3.connectionpool                             [DEBUG  ]  Starting new HTTPS connection (1): api.multiqc.info:443
[2024-05-23 10:34:23] urllib3.connectionpool                             [DEBUG  ]  https://api.multiqc.info:443 "GET /version?version_multiqc=1.22.1&version_python=3.11.6&operating_system=Linux&is_docker=False&is_singularity=False&is_conda=False&is_ci=False&is_notebook=False HTTP/1.1" 200 182
[2024-05-23 10:34:23] multiqc.core.version_check                         [DEBUG  ]  Latest MultiQC version is v1.22.1, released 2024-05-17
[2024-05-23 10:34:23] multiqc.multiqc                                    [DEBUG  ]  Working dir : /lustre/scratch126/pam/teams/team230/wr7/tmp/t_pallidum_rnaseq/prok/nf_rnaseq/multiqc_debugging
[2024-05-23 10:34:23] multiqc.multiqc                                    [DEBUG  ]  Template    : default
[2024-05-23 10:34:23] multiqc.multiqc                                    [DEBUG  ]  Command used: /lustre/scratch126/pam/teams/team230/wr7/tmp/t_pallidum_rnaseq/prok/nf_rnaseq/multiqc_venv/bin/multiqc -n multiqc_report.html -f --config ../config/multiqc/multiqc_config.yml -v .
[2024-05-23 10:34:23] multiqc.core.file_search                           [INFO   ]  Only using modules: fastqc
[2024-05-23 10:34:23] multiqc.core.file_search                           [DEBUG  ]  Analysing modules: fastqc, fastqc
[2024-05-23 10:34:23] multiqc.core.file_search                           [INFO   ]  Search path: /lustre/scratch126/pam/teams/team230/wr7/tmp/t_pallidum_rnaseq/prok/nf_rnaseq/multiqc_debugging
[2024-05-23 10:34:23] multiqc.report                                     [DEBUG  ]  Ignored 332 search patterns as didn't match running modules.
         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 44/44  
[2024-05-23 10:34:23] multiqc.report                                     [DEBUG  ]  Summary of files that were skipped by the search: |skipped_no_match: 28|
[2024-05-23 10:34:23] multiqc.core.exec_modules                          [DEBUG  ]  Running module: fastqc
[2024-05-23 10:34:23] multiqc.base_module                                [DEBUG  ]  fastqc/zip - Skipping 'fastqc/raw/sample_1_REP1_2_fastqc.zip' as it matched the path_filters_exclude for 'FastQC: raw'
[2024-05-23 10:34:23] multiqc.base_module                                [DEBUG  ]  fastqc/zip - Skipping 'fastqc/raw/sample_2_REP1_1_fastqc.zip' as it matched the path_filters_exclude for 'FastQC: raw'
[2024-05-23 10:34:23] multiqc.base_module                                [DEBUG  ]  fastqc/zip - Skipping 'fastqc/raw/sample_1_REP1_1_fastqc.zip' as it matched the path_filters_exclude for 'FastQC: raw'
[2024-05-23 10:34:23] multiqc.base_module                                [DEBUG  ]  fastqc/zip - Skipping 'fastqc/raw/sample_1_REP2_2_fastqc.zip' as it matched the path_filters_exclude for 'FastQC: raw'
[2024-05-23 10:34:23] multiqc.base_module                                [DEBUG  ]  fastqc/zip - Skipping 'fastqc/raw/sample_2_REP2_2_fastqc.zip' as it matched the path_filters_exclude for 'FastQC: raw'
[2024-05-23 10:34:23] multiqc.base_module                                [DEBUG  ]  fastqc/zip - Skipping 'fastqc/raw/sample_1_REP2_1_fastqc.zip' as it matched the path_filters_exclude for 'FastQC: raw'
[2024-05-23 10:34:23] multiqc.base_module                                [DEBUG  ]  fastqc/zip - Skipping 'fastqc/raw/sample_2_REP1_2_fastqc.zip' as it matched the path_filters_exclude for 'FastQC: raw'
[2024-05-23 10:34:23] multiqc.base_module                                [DEBUG  ]  fastqc/zip - Skipping 'fastqc/raw/sample_2_REP2_1_fastqc.zip' as it matched the path_filters_exclude for 'FastQC: raw'
[2024-05-23 10:34:23] multiqc.modules.fastqc.fastqc                      [INFO   ]  Found 8 reports
[2024-05-23 10:34:24] multiqc.plots.plotly.plot                          [DEBUG  ]  Deprecated field 'xDecimals'. Use 'x_decimals' instead
[2024-05-23 10:34:24] multiqc.plots.plotly.plot                          [DEBUG  ]  Deprecated field 'yPlotBands'. Use 'y_bands' instead
[2024-05-23 10:34:24] multiqc.plots.plotly.plot                          [DEBUG  ]  Deprecated field 'xDecimals'. Use 'x_decimals' instead
[2024-05-23 10:34:24] multiqc.plots.plotly.plot                          [DEBUG  ]  Deprecated field 'xPlotBands'. Use 'x_bands' instead
[2024-05-23 10:34:24] multiqc.plots.plotly.plot                          [DEBUG  ]  Deprecated field 'table_title'. Use 'title' instead
[2024-05-23 10:34:24] multiqc.plots.plotly.plot                          [DEBUG  ]  Deprecated field 'xTitle'. Use 'xlab' instead
[2024-05-23 10:34:24] multiqc.plots.plotly.plot                          [DEBUG  ]  Deprecated field 'yTitle'. Use 'ylab' instead
[2024-05-23 10:34:24] multiqc.plots.plotly.plot                          [DEBUG  ]  Deprecated field 'datalabels'. Use 'display_values' instead
[2024-05-23 10:34:24] multiqc.base_module                                [DEBUG  ]  fastqc: deleting attribute self.dup_keys
[2024-05-23 10:34:24] multiqc.base_module                                [DEBUG  ]  fastqc: deleting attribute self.status_colours
[2024-05-23 10:34:24] multiqc.core.exec_modules                          [DEBUG  ]  Running module: fastqc
[2024-05-23 10:34:24] multiqc.base_module                                [DEBUG  ]  fastqc/zip - Selecting 'fastqc/trim/sample_2_REP2_trimmed_2_fastqc.zip' as it matched the path_filters for 'FastQC: trimmed'
[2024-05-23 10:34:24] multiqc.base_module                                [DEBUG  ]  fastqc/zip - Selecting 'fastqc/trim/sample_2_REP1_trimmed_1_fastqc.zip' as it matched the path_filters for 'FastQC: trimmed'
[2024-05-23 10:34:24] multiqc.base_module                                [DEBUG  ]  fastqc/zip - Selecting 'fastqc/trim/sample_1_REP1_trimmed_1_fastqc.zip' as it matched the path_filters for 'FastQC: trimmed'
[2024-05-23 10:34:24] multiqc.base_module                                [DEBUG  ]  fastqc/zip - Selecting 'fastqc/trim/sample_1_REP1_trimmed_2_fastqc.zip' as it matched the path_filters for 'FastQC: trimmed'
[2024-05-23 10:34:24] multiqc.base_module                                [DEBUG  ]  fastqc/zip - Selecting 'fastqc/trim/sample_2_REP1_trimmed_2_fastqc.zip' as it matched the path_filters for 'FastQC: trimmed'
[2024-05-23 10:34:24] multiqc.base_module                                [DEBUG  ]  fastqc/zip - Selecting 'fastqc/trim/sample_1_REP2_trimmed_1_fastqc.zip' as it matched the path_filters for 'FastQC: trimmed'
[2024-05-23 10:34:24] multiqc.base_module                                [DEBUG  ]  fastqc/zip - Selecting 'fastqc/trim/sample_2_REP2_trimmed_1_fastqc.zip' as it matched the path_filters for 'FastQC: trimmed'
[2024-05-23 10:34:24] multiqc.base_module                                [DEBUG  ]  fastqc/zip - Selecting 'fastqc/trim/sample_1_REP2_trimmed_2_fastqc.zip' as it matched the path_filters for 'FastQC: trimmed'
[2024-05-23 10:34:24] multiqc.base_module                                [DEBUG  ]  fastqc/zip - Skipping 'fastqc/raw/sample_1_REP1_2_fastqc.zip' as it didn't match the path_filters for 'FastQC: trimmed'
[2024-05-23 10:34:24] multiqc.base_module                                [DEBUG  ]  fastqc/zip - Skipping 'fastqc/raw/sample_2_REP1_1_fastqc.zip' as it didn't match the path_filters for 'FastQC: trimmed'
[2024-05-23 10:34:24] multiqc.base_module                                [DEBUG  ]  fastqc/zip - Skipping 'fastqc/raw/sample_1_REP1_1_fastqc.zip' as it didn't match the path_filters for 'FastQC: trimmed'
[2024-05-23 10:34:24] multiqc.base_module                                [DEBUG  ]  fastqc/zip - Skipping 'fastqc/raw/sample_1_REP2_2_fastqc.zip' as it didn't match the path_filters for 'FastQC: trimmed'
[2024-05-23 10:34:24] multiqc.base_module                                [DEBUG  ]  fastqc/zip - Skipping 'fastqc/raw/sample_2_REP2_2_fastqc.zip' as it didn't match the path_filters for 'FastQC: trimmed'
[2024-05-23 10:34:24] multiqc.base_module                                [DEBUG  ]  fastqc/zip - Skipping 'fastqc/raw/sample_1_REP2_1_fastqc.zip' as it didn't match the path_filters for 'FastQC: trimmed'
[2024-05-23 10:34:24] multiqc.base_module                                [DEBUG  ]  fastqc/zip - Skipping 'fastqc/raw/sample_2_REP1_2_fastqc.zip' as it didn't match the path_filters for 'FastQC: trimmed'
[2024-05-23 10:34:24] multiqc.base_module                                [DEBUG  ]  fastqc/zip - Skipping 'fastqc/raw/sample_2_REP2_1_fastqc.zip' as it didn't match the path_filters for 'FastQC: trimmed'
[2024-05-23 10:34:24] multiqc.modules.fastqc.fastqc                      [INFO   ]  Found 8 reports
[2024-05-23 10:34:24] multiqc.plots.plotly.plot                          [DEBUG  ]  Deprecated field 'xDecimals'. Use 'x_decimals' instead
[2024-05-23 10:34:24] multiqc.plots.plotly.plot                          [DEBUG  ]  Deprecated field 'yPlotBands'. Use 'y_bands' instead
[2024-05-23 10:34:24] multiqc.plots.plotly.plot                          [DEBUG  ]  Deprecated field 'xDecimals'. Use 'x_decimals' instead
[2024-05-23 10:34:24] multiqc.plots.plotly.plot                          [DEBUG  ]  Deprecated field 'xPlotBands'. Use 'x_bands' instead
[2024-05-23 10:34:24] multiqc.plots.plotly.plot                          [DEBUG  ]  Deprecated field 'table_title'. Use 'title' instead
[2024-05-23 10:34:24] multiqc.plots.plotly.plot                          [DEBUG  ]  Deprecated field 'xTitle'. Use 'xlab' instead
[2024-05-23 10:34:24] multiqc.plots.plotly.plot                          [DEBUG  ]  Deprecated field 'yTitle'. Use 'ylab' instead
[2024-05-23 10:34:24] multiqc.plots.plotly.plot                          [DEBUG  ]  Deprecated field 'datalabels'. Use 'display_values' instead
[2024-05-23 10:34:24] multiqc.base_module                                [DEBUG  ]  fastqc-1: deleting attribute self.dup_keys
[2024-05-23 10:34:24] multiqc.base_module                                [DEBUG  ]  fastqc-1: deleting attribute self.status_colours
[2024-05-23 10:34:24] multiqc.core.software_versions                     [DEBUG  ]  Reading software versions from config.software_versions
[2024-05-23 10:34:24] multiqc.core.file_search                           [INFO   ]  Only using modules: fastqc
[2024-05-23 10:34:24] multiqc.report                                     [DEBUG  ]  Wrote data file fastqc_sequence_counts_plot.txt
[2024-05-23 10:34:24] multiqc.report                                     [DEBUG  ]  Wrote data file fastqc_per_base_sequence_quality_plot.txt
[2024-05-23 10:34:24] multiqc.report                                     [DEBUG  ]  Wrote data file fastqc_per_sequence_quality_scores_plot.txt
[2024-05-23 10:34:24] multiqc.report                                     [DEBUG  ]  Wrote data file fastqc_per_sequence_gc_content_plot_Percentages.txt
[2024-05-23 10:34:24] multiqc.report                                     [DEBUG  ]  Wrote data file fastqc_per_sequence_gc_content_plot_Counts.txt
[2024-05-23 10:34:24] multiqc.report                                     [DEBUG  ]  Wrote data file fastqc_per_base_n_content_plot.txt
[2024-05-23 10:34:24] multiqc.report                                     [DEBUG  ]  Wrote data file fastqc_sequence_length_distribution_plot.txt
[2024-05-23 10:34:24] multiqc.report                                     [DEBUG  ]  Wrote data file fastqc_sequence_duplication_levels_plot.txt
[2024-05-23 10:34:24] multiqc.report                                     [DEBUG  ]  Wrote data file fastqc_overrepresented_sequences_plot.txt
[2024-05-23 10:34:24] multiqc.report                                     [DEBUG  ]  Wrote data file fastqc_top_overrepresented_sequences_table.txt
[2024-05-23 10:34:24] multiqc.report                                     [DEBUG  ]  Wrote data file fastqc_adapter_content_plot.txt
[2024-05-23 10:34:24] multiqc.report                                     [DEBUG  ]  Wrote data file fastqc-status-check-heatmap.txt
[2024-05-23 10:34:24] multiqc.plots.plotly.plot                          [DEBUG  ]  Deprecated field 'table_title'. Use 'title' instead
[2024-05-23 10:34:24] multiqc.report                                     [DEBUG  ]  Wrote data file multiqc_general_stats.txt
[2024-05-23 10:34:24] multiqc.core.write_results                         [DEBUG  ]  Moving data file from '/tmp/tmpbf7v6zda/multiqc_data' to '/lustre/scratch126/pam/teams/team230/wr7/tmp/t_pallidum_rnaseq/prok/nf_rnaseq/multiqc_debugging/multiqc_report_data'
[2024-05-23 10:34:24] multiqc.core.write_results                         [INFO   ]  Data        : multiqc_report_data
[2024-05-23 10:34:24] multiqc.core.write_results                         [DEBUG  ]  Compressing plot data
[2024-05-23 10:34:25] multiqc.core.write_results                         [INFO   ]  Report      : multiqc_report.html
[2024-05-23 10:34:25] multiqc.core.write_results                         [DEBUG  ]  Full report path: /lustre/scratch126/pam/teams/team230/wr7/tmp/t_pallidum_rnaseq/prok/nf_rnaseq/multiqc_debugging/multiqc_report.html
[2024-05-23 10:34:25] multiqc.multiqc                                    [INFO   ]  MultiQC complete

Before submitting

• I have read the troubleshooting documentation.
• I am using the latest release of MultiQC.
• I have included a full MultiQC log, not truncated.
• I have attached an input file (.zip if necessary) that triggers the error.

[MatthiasZepper]

I can confirm this issue and ran into it while troubleshooting the reports for the nf-core/rnaseq pipeline.

If that helps with troubleshooting: The module is still present twice in the General Statistics table, but the second instance is not present in the main report and navigation bar. Setting a custom anchor in the config in addition to a custom name did not help either, so what is described in the docs here is no longer working. I tested with version 1.18 and there things were still fine.

[MatthiasZepper]

Just in case a screenshot helps:

MultiQC 1.23dev, 1.22, 1.21	MultiQC 1.18
Screenshot of Navbar 1.23dev	Screenshot of Navbar 1.18

[vladsavelyev]

This a nasty bug, sorry about this. It should be now fixed with: #2592

I'll make a patch release later.

[FerranLlobetC]

Hi,
Today I encountered the same problem using version 1.23.dev0. Also in version 1.22. As @MatthiasZepper commented above, when downgrading to version 1.18 everything worked as expected.