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Introduction

Bioinformatics projects often include non-standardised analyses, with results from custom scripts or in-house packages. It can be frustrating to have a MultiQC report describing results from 90% of your pipeline but missing the final key plot. To help with this, MultiQC has a special "custom content" module.

Custom content parsing is a little more restricted than standard modules. Specifically:

  • Only one plot per section is possible
  • Plot customisation is more limited

All plot types can be generated using custom content - see the test files for examples of how data should be structured.

Use the name custom_content to refer to this module within configuration settings that require a module name, such as module_order or run_modules.

Data from a released tool​

If your data comes from a released bioinformatics tool, you shouldn't be using this feature of MultiQC! Sure, you can probably get it to work, but it's better if a fully-fledged core MultiQC module is written instead. That way, other users of MultiQC can also benefit from results parsing.

Note that proper MultiQC modules are more robust and powerful than this custom-content feature. You can also write modules in MultiQC plugins if they're not suitable for general release.

Images​

As of MultiQC v1.7, you can import custom images into your MultiQC reports. Simply add _mqc to the end of the filename for .png, .jpg or .jpeg files, for example: my_image_file_mqc.png or summmary_diagram.jpeg.

Images will be embedded within the HTML file, so will be self contained. Note that this means that it's very possible to make the HTML file very very large if abused!

The report section name and description will be automatically based on the filename.

Note that if you are using sp: to take in images with a custom filename you need to also set ignore_images: false in your config. For example:

custom_data:
  my_custom_content_image:
    section_name: "My nice image"
sp:
  my_custom_content_image:
    fn: "*.png"
ignore_images: false

MultiQC-specific data file​

If you can choose exactly how your data output looks, then the easiest way to parse it is to use a MultiQC-specific format. If the filename ends in *_mqc.(yaml|yml|json|txt|csv|tsv|log|out|png|jpg|jpeg|html) then it will be found by any standard MultiQC installation with no additional customisation required.

These files contain configuration information specifying how the data should be parsed, alongside the data. If you want to use YAML, this is an example of how it should look:

id: "my_pca_section"
section_name: "PCA Analysis"
description: "This plot shows the first two components from a principal component analysis."
plot_type: "scatter"
pconfig:
  id: "pca_scatter_plot"
  title: "PCA Plot"
  xlab: "PC1"
  ylab: "PC2"
data:
  sample_1: { x: 12, y: 14 }
  sample_2: { x: 8, y: 6 }
  sample_3: { x: 5, y: 11 }
  sample_4: { x: 9, y: 12 }

This example YAML file is data only, and is not to be confused with a config file (though the two look very similar). See the docs Data as part of MultiQC config for more on that.

The file format can also be JSON:

{
  "id": "custom_data_lineplot",
  "section_name": "Custom JSON File",
  "description": "This plot is a self-contained JSON file.",
  "plot_type": "linegraph",
  "pconfig": {
    "id": "custom_data_linegraph",
    "title": "Output from my JSON file",
    "ylab": "Number of things",
    "xDecimals": false
  },
  "data": {
    "sample_1": { "1": 12, "2": 14, "3": 10, "4": 7, "5": 16 },
    "sample_2": { "1": 9, "2": 11, "3": 15, "4": 18, "5": 21 }
  }
}

Note that if you're using plot_type: html then data just takes a string, with no sample keys.

For maximum compatibility with other tools, you can also use comma-separated or tab-separated files. Include commented header lines with plot configuration in YAML format:

# id: "Output from my script'
# section_name: 'Custom data file'
# description: 'This output is described in the file header. Any MultiQC installation will understand it without prior configuration.'
# format: 'tsv'
# plot_type: 'bargraph'
# pconfig:
#    id: 'custom_bargraph_w_header'
#    ylab: 'Number of things'
Category_1    374
Category_2    229
Category_3    39
Category_4    253

You can easily inject custom HTML snippets by ending the filename with _mqc.html - again the embedded config works in a similar way, but with a HTML comment:

<!--
id: 'custom-html'
section_name: 'Custom HTML'
description: 'This section is created using a custom HTML file'
-->
<p>Some custom HTML content here.</p>

If no configuration is given, MultiQC will do its best to guess how to visualise your data appropriately. To see examples of typical file structures which are understood, see the test data used to develop this code. Something will be probably be shown, but it may produce unexpected results.

Check Tricky extras for certain caveats about formatting headers for custom tsv or csv files, particularly for the first column.

Data as part of MultiQC config​

If you are already using a MultiQC config file to add data to your report (for example, titles / introductory text), you can give data within this file too. This can be in any MultiQC config file (for example, passed on the command line with -c my_yaml_file.yaml or in your launch directory as multiqc_config.yml - see Configuration).

This is not to be confused with the YAML data files described in the above section, MultiQC-specific data file. For example, MultiQC config files will not be found with _mqc.yml file extensions.

This is useful as you can keep everything contained within a single file (including stuff unrelated to this specific custom content feature of MultiQC).

To be understood by MultiQC, the custom_data key must be found. This must contain a section with a unique id, specific to your new report section. Finally, the contents of this second dictionary will look the same as the above stand-alone YAML files. For example:

custom_data:
  my_data_type:
    id: "mqc_config_file_section"
    section_name: "My Custom Section"
    description: "This data comes from a single multiqc_config.yaml file"
    plot_type: "bargraph"
    pconfig:
      id: "barplot_config_only"
      title: "MultiQC Config Data Plot"
      ylab: "Number of things"
    data:
      sample_a:
        first_thing: 12
        second_thing: 14
      sample_b:
        first_thing: 8
        second_thing: 6
      sample_c:
        first_thing: 11
        second_thing: 5
      sample_d:
        first_thing: 12
        second_thing: 9

Or to add data to the General Statistics table:

custom_data:
  my_genstats:
    plot_type: "generalstats"
    pconfig:
      - col_1:
          max: 100
          min: 0
          scale: "RdYlGn"
          suffix: "%"
      - col_2:
          min: 0
    data:
      sample_a:
        col_1: 14.32
        col_2: 1.2
      sample_b:
        col_1: 84.84
        col_2: 1.9

Use a list of headers in pconfig (keys prepended with -) to specify the order of columns in the General Statistics table.

See the general statistics docs for more information about configuring data for the General Statistics table.

Separate configuration and data files​

It's not always possible or desirable to include MultiQC configuration within a data file. If this is the case, you can add to the MultiQC configuration to specify how input files should be parsed.

As described in the Data as part of MultiQC config section, this configuration should be held within a section called custom_data with a section-specific id. The only difference is that no data subsection is given and a search pattern for the given id must be supplied.

Search patterns are added as with any other module. Ensure that the search pattern key is the same as your custom_data section ID.

For example, a MultiQC config file could look as follows:

# Other MultiQC config stuff here
custom_data:
  example_files:
    file_format: "tsv"
    section_name: "Coverage Decay"
    description: "This plot comes from files acommpanied by a multiqc_config.yaml file for configuration"
    plot_type: "linegraph"
    pconfig:
      id: "example_coverage_lineplot"
      title: "Coverage Decay"
      ylab: "X Coverage"
      ymax: 100
      ymin: 0
sp:
  example_files:
    fn: "example_files_*"

And work with the following data file: example_files_Sample_1.txt:

0	98.22076066
1	97.96764159
2	97.78227175
3	97.61262195
# [...]

This kind of customisation should work with most Custom Content types. For example, using an image called some_science_mqc.jpeg gives us a report section some_science, which we can then add a nicer name and description to:

custom_data:
  some_science:
    section_name: "Some real science"
    description: "This description comes from multiqc_config.yaml and helps to annotate the Custom Content image."

If no configuration is given, MultiQC will do its best to guess how to visualise your data appropriately. To see examples of typical file structures which are understood, see the test data used to develop this code.

Configuration

Grouping sections and subsections​

If you have multiple content types that you would like to group together with MultiQC sub-sections, you can do so using the following keys:

parent_id: custom_section
parent_name: "Some grouped data"
parent_description: "This parent section contains one or more sub-sections below it"

Any custom-content files that share the same parent_id will be grouped.

Note that some things, such as parent_name are taken from the first file that MultiQC finds with this parent_id. So it's a good idea to specify this in every file. parent_description and extra is taken from the first file where it is set.

parent_id only works within Custom Content. It is not currently possible to add custom content output into a report section from a core MultiQC module.

Order of sections​

If you have multiple different Custom Content sections, their order will be random and may vary between runs. To avoid this, you can specify an order in your MultiQC config as follows:

custom_content:
  order:
    - first_cc_section
    - second_cc_section

Each section name should be the ID assigned to that section. You can explicitly set this (see below), or the Custom Content module will automatically assign an ID. To find out what your custom content section ID is, generate a report and click the side navigation to your section. The browser URL should update and show something that looks like this:

multiqc_report.html#my_cc_section

The section ID is the part after the # (my_cc_section in the above section).

Note that any Custom Content sections found that are not specified in the config will be placed at the top of the report.

Section configuration​

See below for how these config options can be specified (either within the data file or in a MultiQC config file). All of these configuration parameters are optional, and MultiQC will do its best to guess sensible defaults if they are not specified.

All possible configuration keys and their default values are shown below:

id: null # Unique ID for report section.
section_anchor: <id> # Used in report section #soft-links
section_name: <id> # Nice name used for the report section header
section_href: null # External URL for the data, to find more information
description: null # Introductory text to be printed under the section header
section_extra: null # Custom HTML to add after the section description
file_format: null # File format of the data (eg. csv / tsv)
plot_type:
  null # The plot type to visualise the data with.
  # generalstats | table | bargraph | linegraph | boxplot | scatter | heatmap | violin
pconfig: {} # Configuration for the plot.

Data types generalstats and violin are only possible by setting the above configuration keys (these can't be guessed by data format).

Note that any custom content data found with the same section id will be merged into the same report section / plot. The other section configuration keys are merged for each file, with identical keys overwriting what was previously parsed.

This approach means that it's possible to have a single file containing data for multiple samples, but it's also possible to have one file per sample and still have all of them summarised.

If you're using plot_type: 'generalstats' then a report section will not be created and most of the configuration keys above are ignored.

Plot configuration​

Configuration of specific plots follows the same syntax as used when writing modules. To find out more, please see the later docs. Specifically, the plot config docs for bar graphs, line graphs, box plots, scatter plots, tables, violin plots and heatmaps.

Wherever you see pconfig, any key can be used within the above syntax.

Tricky extras​

Because of the way this module works, there are a few specifics that can trip you up. Most of these should probably be fixed one day. Feel free to ask for help on the community forum, or submit a pull request! I'll try to keep a list here to help the wary...

Differences between Tables and General Stats​

Although they're both tables, note that general stats configures columns with a list in the pconfig scope (see above example). Files that are just tables use headers instead.

First columns in tables are special​

The first column in every table is reserved for the sample name. As such, it shouldn't contain data. All header configuration will be ignored for the first column. The only exception is name: this can be tweaked using the somewhat tricky col1_header field in the pconfig scope (see table docs). Alternatively, you can customise the column name by including a 'header row' in the first line of the tsv or csv itself specifying the column names, with the first column with the name of your choice, and subsequent columns including the key(s) defined in the header.

Linting​

MultiQC has been developed to be as forgiving as possible and will handle lots of invalid or ignored configurations. This is useful for most users but can make life difficult when getting MultiQC to work with a new custom content format.

To help with this, you can run MultiQC with the --strict flag, which will give explicit warnings about anything that is not optimally configured. For example:

multiqc --strict test-data

You can alternatively enable the strict mode by setting the environment variable MULTIQC_STRICT, or by setting it into the config: strict: true.

Examples

Probably the best way to get to grips with Custom Content is to see some examples. The MultiQC automated testing runs with a number of different files which you can look through for inspiration.

For example, to see a file which generates a table in a report by itself, you can have a look at embedded_config/table_headers_mqc.txt (link).