qc-seq
======

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 JSON file with statistics.

Configuration
-------------
Example
^^^^^^^
.. literalinclude:: ../../test/data/config/qc-seq.json
   :language: json

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

.. list-table:: Configuration options
   :header-rows: 1

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