Disable mean read length in picard

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Hi there,

I’d like to remove mean read length under the picard report.

Screenshot 2024-05-07 at 11.57.24 AM
Screenshot 2024-05-07 at 11.57.24 AM810×582 33.4 KB

I’ve my config file as:

show_analysis_paths: False

sp:
 picard/quality_by_cycle:
  skip: true
 picard/quality_by_cycle:
  skip: true
 picard/quality_score_distribution:
  skip: true
 picard/insert_size_metrics:
  skip: true

Example of such report:

There is no flag on following tutorials to disable mean read length metric:

multiqc v1.21

There’s no read length metrics file either generated by gatk collect metrics. However, there’s read_length_histogram.pdf file generated.

Please let me know if anymore information is required.

2

The term you’re looking for here is “section”. MultiQC reports are grouped into module (tool) and each heading under that is a section.

Sections can be removed by ID without changing the files that are parsed. See " Removing modules or sections" in the docs:

If you would like to remove just one section of a module report, you can do so with the remove_sections config option as follows:

remove_sections:
 - section-id-one
 - second-section-id

:bulb: Tip
The section ID is the string appended to the URL when clicking a report section in the navigation.

For example, the GATK module has a section with the title “Compare Overlap”. When clicking that in the report’s left hand side navigation, the web browser URL has #gatk-compare-overlap appended. Here, you would add gatk-compare-overlap to the remove_sections config.

So in your case your config would look something like this:

remove_sections:
  - picard_alignment_readlength

Regarding your example report:

I can’t see a “Mean read length” section here, so I’m a little confused. It was generated with MultiQC v1.9 which is very old now (released 2020), so it’s possible that MultiQC didn’t support this plot type back then.

I hope this helps!

Phil

3

Thank you, it worked and helped.
My config file looks as below:

show_analysis_paths: False

sp:
 picard/quality_by_cycle:
  skip: true
 picard/quality_score_distribution:
  skip: true
 picard/insert_size_metrics:
  skip: true
remove_sections:
 - picard_alignment_readlength
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