MultiQC plugin interacting with the Illumina Genologics Clarity LIMS
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multiqc_clarity
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README.md

MultiQC_Clarity is a plugin for MultiQC, able to insert project-level and sample-level metadata from the BaseSpace Clarity LIMS into MultiQC Reports

For more information about MultiQC, see http://multiqc.info

For more information about BaseSpace Clarity LIMS, see https://www.genologics.com/clarity-lims/

Description

MultiQC_Clarity connects to your Clarity LIMS installation using the API. MultiQC runs as normal, generating a list of sample names based on the contents of the files found. These sample names are passed to the MultiQC_Clarity plugin, which searches your Clarity LIMS installation for matching sample names. If exact matches are found, then the metadata configured in the config file is retrieved and entered into the report.

Installation

Plugin Installation

This plugin will hopefully soon be available on the Python Package Index. Until then, you can install it from GitHub directly using pip:

pip install --upgrade --force-reinstall git+https://github.com/MultiQC/MultiQC_Clarity.git

Alternatively, you can download or clone this repository and install it manually:

python setup.py install

Genologics Package

The MultiQC_Clarity plugin uses the Genologics Python package, available on PyPI. This needs to be configured first. Create a file called .genologicsrc in your user's home directory that looks as follows:

[genologics]
BASEURI=https://your.installation.com
USERNAME=[YOUR-USERNAME]
PASSWORD=[YOUR-PASSWORD]

Configuration

Before MultiQC_Clarity will work with MultiQC, you need to tell it what information to retrieve from the LIMS. Unfortunately, as every Clarity installation is different from the next, this cannot be automated.

To do this, you need to add to your MultiQC configuration. See the main MultiQC documentation for more information on how to do this. For a single run, you can just create a file called multiqc_config.yaml in the working directory.

See the bundled multiqc_config_example.yaml file to see a real-life example of this.

There are three parts in the MultiQC report where you can add content - the report header (typically project-level information), the General Statistics table and as a section in the report. The required configuration is broken into the same three sections.

Next, you need to specify which Clarity LIMS entity you want to retrieve information from. This can be Project, Sample or the name of a step.

If Project or Sample, the next level of configuration is the UDF name that you want to load. If it's a step, you need to specify either outputs or inputs.

For example, a basic setup with minimal configuration could be:

clarity:
    report_header_info:
        Project:
            'custom UDF name':
            'another custom UDF':
    general_stats:
        Sample:
            'a custom UDF':
    clarity_module:
        'custom step name':
            'inputs':
                'your UDF name':

The final level of configuration configures how MultiQC handles the data itself. You can read the main MultiQC documentation for more details, or see the above example for more information.

One special config param not usually available is multiply_by. For example, to display a count in for Millions, set multiply_by: 0.000001. To display a fraction as a percent, set multiply_by: 100.

Usage

Once installed and configured the plugin should run automtically.

--clarity_project

If you know the project for this run, you can specify its LUID manually to MultiQC_Clarity. This then ignores the samples found in the report and just grabs data from all samples in the specified project.

--clarity_skip_name_editing

By default, MultiQC_Clarity removes the following strings from sample names before searching for them in the LIMS: _1, _2, _R1, _R2. Use this command line flag to disable this behaviour.

--disable_clarity

This command line flag prevents the MultiQC_Clarity plugin from running on this MultiQC run.

Contributors

  • MultiQC_Clarity lead and main author: @Galithil
  • MultiQC lead and main author: @ewels
  • MultiQC_Clarity code contributions and testing help from: @ewels