Section_comments showed twice, section_name doesn't follow the setting

[Hanjiewu]

Hi, I am having some problems while customizing data using MultiQC v1.25.1:
Here is my mini multiqc_config.yaml:

skip_generalstats: true

exclude_modules:
  - prokka

custom_data:
    Pangenome_Phylogeny:
      section_name: 'Pangenome Phylogeny'
       
    Pangenome_profile:
      section_name: 'Pangenome profile'

    Pangenome_frequency:
      section_name: 'Pangenome frequency'

    Intergenic_region_core_SNP:
        section_name: 'Core Intergenic region SNPs'
        plot_type: 'table'

section_comments: 
  Intergenic_region_core_SNP: "Core intergenic region SNP report: <br />  
    The SNP_Position refers to the actual position identified in the Prokka annotation. For individual strains, the report format is as follows: <br />  
    `Gene_1(annotation)_+_+_IGR_Cluster_ID_SNP_range_+_+_Gene_2(annotation)_+_+_X`, where X can be: <br /> 
  <ul><li>DP: Double Promoter <---- IGR ----> genes are divergently transcribed.</li>  
      <li>DT: Double Terminator ----> IGR <---- genes are convergently transcribed.</li>
      <li>CO_F: Co-oriented Forward ----> IGR ----> genes are co-oriented forward.</li>
      <li>CO_R: Co-oriented Reverse <---- IGR <---- genes are co-oriented reverse.</li></ul>
    Note: `_+_+_` is used as a delimiter between fields. If the IGR is at the edge of a contig, only one flanking gene may exist, and in such cases, `NA` will be used to replace the gene and orientation information."

sp:
    Intergenic_region_core_SNP:
        fn: 'IGR_coreSNP.tsv'
    Pangenome_Phylogeny:
        fn: 'pangenome_matrix.png'
    Pangenome_profile:
        fn: 'pangenome_pie.png'
    Pangenome_frequency:
        fn: 'pangenome_frequency.png'

ignore_images: false          
         

Issues:

1. section_comments is showing up twice:
   The section comments for Intergenic_region_core_SNP appear twice under the section name “Core Intergenic Region SNPs.”

2. section_name doesn’t follow the settings for images:
   Although the section names of Pangenome_Phylogeny, Pangenome_profile and Pangenome frequency were set as “Pangenome Phylogeny”, “Pangenome Profile” and “Pangenome frequency”, they appear as “pangenome”, “pangenome pie” and “pangenome frequency” in the report.

3. Issues with custom_plot_config and custom_table_header_config:
   The issue raised earlier regarding custom_plot_config and custom_table_header_config not working persists. Custom_plot_config and custom_table_header_config not working

[vlad.savelyev]

Hi Hanjiewu,

Thank you for bringing up those issues with us, and sorry for the poor experience.

Going through both topics here:

1. section_comments is showing up twice:
   The section comments for Intergenic_region_core_SNP appear twice under the section name “Core Intergenic Region SNPs.”

It’s a but that happens because the comment matches both a section and the whole module IDs. I fixed it now with this change: Avoid showing `section_comment` both for module and section when they have the same ID (that is, in custom content) by vladsavelyev · Pull Request #2954 · MultiQC/MultiQC · GitHub

2. section_name doesn’t follow the settings for images:
   Although the section names of Pangenome_Phylogeny, Pangenome_profile and Pangenome frequency were set as “Pangenome Phylogeny”, “Pangenome Profile” and “Pangenome frequency”, they appear as “pangenome”, “pangenome pie” and “pangenome frequency” in the report.

This issue was actually fixed just lately with this change: Custom content image: support custom_data config with section name etc, fix misleading logging by vladsavelyev · Pull Request #2939 · MultiQC/MultiQC · GitHub

3. Issues with custom_plot_config and custom_table_header_config:
   The issue raised earlier regarding custom_plot_config and custom_table_header_config not working persists. Custom_plot_config and custom_table_header_config not working

The docs are misleading: it should actually say:

custom_table_header_config:
    "Intergenic region core SNP":
        "SNP Position":
            format: "{:,d}"

That is, the column header that appears in the table is expected there, plus the table ID that you have in your pconfig (“Intergenic region core SNP”).

I fixed the docs with Configure `custom_table_header_config`: fix docs, support both the old and the new ways by vladsavelyev · Pull Request #2955 · MultiQC/MultiQC · GitHub, however, we want to support the other way to configure that too - did so in the same pull-request.

Hopefully with all these updates, the issues you reported will be resolved.

Thank you so much for reporting!