MultiQC
=======

Overview
--------

MultiQC searches a project directory for analysis logs and report files
generated by a wide range of bioinformatics tools, then compiles the results
into a single interactive HTML report. It supports over 150 tools including
FastQC, fastp, STAR, Picard, Salmon, featureCounts, and many more. MultiQC
makes it easy to compare metrics across all samples in a project at a glance.

Installation
------------

.. code-block:: bash

   mamba install -c bioconda multiqc

Basic Usage
-----------

Run MultiQC on an entire project directory to automatically discover and
aggregate all supported report files.

.. code-block:: bash

   # Run MultiQC on an entire project directory
   multiqc /project/results/ -o /project/multiqc_report/

   # Run with specific module selection and title
   multiqc . --module fastqc --module star --module picard \
     --title "RNA-seq QC Report" -o qc_report/

Key Parameters
--------------

.. list-table::
   :header-rows: 1
   :widths: 30 70

   * - Flag / option
     - Description
   * - ``-o``
     - Output directory for the report (default: current directory).
   * - ``--module``
     - Run only the specified modules. Repeat for multiple modules.
   * - ``--title``
     - Report title shown in the HTML header.
   * - ``-f`` / ``--force``
     - Overwrite existing reports in the output directory.
   * - ``-d`` / ``--dirs``
     - Prepend sample names with the directory path for disambiguation.
   * - ``-x`` / ``--exclude``
     - Exclude specific modules from the report.
   * - ``--ignore``
     - Ignore files or directories matching the given glob pattern.
   * - ``-c`` / ``--config``
     - Path to a YAML configuration file for customising report behaviour.
   * - ``--flat``
     - Use static plot images instead of interactive plots.
   * - ``--export``
     - Export plot data as tab-separated files alongside the report.

Expected Output
---------------

MultiQC creates the following files in the output directory:

* ``multiqc_report.html`` -- an interactive HTML report with plots and tables
  summarising metrics from all discovered tools and samples.
* ``multiqc_data/`` -- a directory containing tab-separated data files for
  every module, a ``multiqc_general_stats.txt`` table, and the parsed log
  data in JSON format.

The HTML report includes a general statistics table, per-module sections
with interactive plots, and a toolbar for searching, highlighting, and
hiding specific samples.

See Also
--------

* :doc:`fastqc` -- quality control reports that MultiQC can aggregate
* :doc:`fastp` -- preprocessing reports that MultiQC can aggregate
* :doc:`/tools/alignment/star` -- RNA-seq aligner whose logs MultiQC parses