# Disable mean read length in picard

**URL:** <https://community.seqera.io/t/disable-mean-read-length-in-picard/741>\
**Category:** Ask for help\
**Tags:** multiqc, picard\
**Created:** [May 7, 2024, 4:00pm UTC](https://community.seqera.io/t/disable-mean-read-length-in-picard/741 "2024-05-07T16:00:19Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![complexgenome](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/complexgenome/32/392_2.png) [@complexgenome](https://community.seqera.io/u/complexgenome)\
**Post date:** [May 7, 2024, 4:00pm UTC](https://community.seqera.io/t/disable-mean-read-length-in-picard/741/1 "2024-05-07T16:00:19Z")

</div>

Hi there,

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

 ![Screenshot 2024-05-07 at 11.57.24 AM](https://europe1.discourse-cdn.com/flex013/uploads/seqera/original/1X/013df91621e1e7982f84781a028d3c5afa08cc7b.png)

I’ve my config file as:

```auto
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:

> **[MultiQC Report](https://bioinformatics-core-shared-training.github.io/Bulk_RNAseq_Course_2021/additional_scripts/Alignment_QC_Report.html)**
>
> MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report

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

> **[Configuration - MultiQC](https://multiqc.info/docs/getting_started/config/)**
>
> Settings to tweak how MultiQC works

> <https://github.com/MultiQC/MultiQC/blob/f720d81ba5f3d34d7752464caeba0d3adbd5c070/docs/modules/picard.md>

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.

---

<div class="post-metadata">

**Author:** ![ewels](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/ewels/32/1_2.png) [@ewels](https://community.seqera.io/u/ewels)\
**Post date:** [May 8, 2024, 5:23pm UTC](https://community.seqera.io/t/disable-mean-read-length-in-picard/741/2 "2024-05-08T17:23:45Z")

</div>

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:
> 
> ```yaml
> remove_sections:
> - section-id-one
> - second-section-id
> 
> ```
> 
> > 💡 **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.

> **[Customising Reports - MultiQC](https://multiqc.info/docs/reports/customisation/#removing-modules-or-sections)**
>
> Making MultiQC reports bespoke for your use case

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

```yaml
remove_sections:
  - picard_alignment_readlength

```

Regarding your example report:

> [@complexgenome](#):
>
> Example of such report:
> 
> [MultiQC Report](https://bioinformatics-core-shared-training.github.io/Bulk_RNAseq_Course_2021/additional_scripts/Alignment_QC_Report.html)

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

---

<div class="post-metadata">

**Author:** ![complexgenome](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/complexgenome/32/392_2.png) [@complexgenome](https://community.seqera.io/u/complexgenome)\
**Post date:** [May 21, 2024, 9:46pm UTC](https://community.seqera.io/t/disable-mean-read-length-in-picard/741/3 "2024-05-21T21:46:50Z")

</div>

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

```auto
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

```