Custom content being rendered as barplot even though table specified in config

[drpatelh]

Even though I am explicitly specifying plot_type: 'table' in my config file one of the tsv files is being added to the report as a bargraph. The rest of the config associated with that section seems to be rendered as defined except for the plot_type. Something is being overriden somewhere it seems but I cant put my finger on it.

[INFO   ]  custom_content : summary_variants_metrics: Found 2 samples (bargraph)
[INFO   ]  custom_content : summary_assembly_metrics: Found 2 samples (table)

I have attached a minimal test example to reproduce the error below:
test_multiqc.tar.gz

Tested on v1.9.dev0

[ewels]

Ok, after a bit of fiddling I got to the bottom of this. There was some functionality essentially missing from MultiQC to allow you to configure _mqc.tsv files from the custom_data configuration, which I've addressed (I think it would have been fine if you'd put the config in the file headers?). There was also a bit of over-configuration going on.

Here's my working version of your config file:

report_comment: >
    This report has been generated by the <a href="https://github.com/nf-core/viralrecon" target="_blank">nf-core/viralrecon</a>
    analysis pipeline. For information about how to interpret these results, please see the
    <a href="https://github.com/nf-core/viralrecon" target="_blank">documentation</a>.

data_format: 'yaml'

run_modules:
    - custom_content

custom_data:
    summary_variants_metrics:
        section_name: 'Variant calling metrics'
        description: 'generated by the nf-core/viralrecon pipeline'
        plot_type: 'table'
        pconfig:
            id: 'summary_variants_metrics_plot'
            table_title: 'Variant calling metrics'
            namespace: 'Variant calling metrics'
    summary_assembly_metrics:
        section_name: 'De novo assembly metrics'
        description: 'generated by the nf-core/viralrecon pipeline'
        plot_type: 'table'
        pconfig:
            id: 'summary_assembly_metrics_plot'
            table_title: 'De novo assembly metrics'
            namespace: 'De novo assembly metrics'

Changes:

• Removed the sp section - it wasn't needed as the filenames already end _mqc.tsv
• Removed id and file_format as they are the same as the filename, so not needed
• Changed the plot id so that it is unique and not the same as the section id
• Added table_title for the nice table configuration modal windows
• Removed path_filters as they weren't doing anything

I think that was it.. Good bug hunting though, thanks! Hopefully you'll have more luck with this now.

Phil

[drpatelh]

Love it and it works now and thank you!

[ewels]

Ok, I just added a new table config option only_defined_headers so now you can override table wide defaults without losing the other columns. Your config above now looks like this:

custom_data:
    summary_variants_metrics:
        section_name: 'Variant calling metrics'
        description: 'generated by the nf-core/viralrecon pipeline'
        plot_type: 'table'
        pconfig:
            id: 'summary_variants_metrics_plot'
            table_title: 'Variant calling metrics'
            namespace: 'Variant calling metrics'
            format: '{:.0f}'
            only_defined_headers: false
        headers:
            '% Mapped reads (viral)':
                suffix: '%'
    summary_assembly_metrics:
        section_name: 'De novo assembly metrics'
        description: 'generated by the nf-core/viralrecon pipeline'
        plot_type: 'table'
        pconfig:
            id: 'summary_assembly_metrics_plot'
            table_title: 'De novo assembly metrics'
            namespace: 'De novo assembly metrics'
            format: '{:.0f}'

And your tables look like this:

(NB: % Mapped reads (viral) now has a percentage symbol suffix to each value).

[drpatelh]

BOOOOOOMMMM!!