qc-seq module
=============

The ``qc-seq`` module is responsible for removing adapter sequences and low
quality reads, and generating read-level statistics. It also merges the FastQ
files per sample, so they can be used by the other modules. Every set of FastQ
files can be analysed in parallel.

Tools
-----
This module uses `cutadapt <https://cutadapt.readthedocs.io/en/stable/>`_ to remove adapter sequences and low quality bases.
`Sequali <https://sequali.readthedocs.io/en/stable/>`_ is used to generate detailed quality statistics.

Input
-----
The input for this module is one or more pairs of FastQ files per sample, specified in a PEP configuration file, as is shown below.

.. csv-table:: Example input for the qc-seq module
   :delim: ,
   :file: ../../test/pep/chrM-trio-subsamples.csv

Output
------
The output of this module are one set of merged FastQ files per sample, as well as a quality report generated by MultiQC.

Configuration
-------------
You can automatically generate a configuration for the qc-seq module using the ``utilities/create-config.py`` script.

Example
^^^^^^^
.. code:: bash

  $ python3 utilities/create-config.py --module qc-seq HAMLET-data

  {
   "forward_adapter": "AGATCGGAAGAG",
   "reverse_adapter": "AGATCGGAAGAG"
  }

Configuration options
^^^^^^^^^^^^^^^^^^^^^
The only configurable options for this module are the adapter sequences for
`cutadapt <https://cutadapt.readthedocs.io/en/stable/>`_ to remove.

.. list-table:: Configuration options
  :widths: 25 80 20
  :header-rows: 1

  * - Option
    - Description
    - Required
  * - forward_adapter
    - The forward adapter sequence
    - yes
  * - reverse_adapter
    - The reverse adapter sequence
    - yes