.. _home-page-moptail:

*******************
MOP_DNA
*******************

.. autosummary::
   :toctree: generated

This pipeline takes as input the output from MOP_PREPROCESS and it outputs the SNPs and SVs together with their annotation. 


.. image:: ../img/flow_dna.png
  :width: 600
  :alt: mop_dna graph


Input Parameters
======================

The input parameters are stored in yaml files like the one represented here:

.. literalinclude:: ../mop_dna/params.yaml
   :language: yaml



How to run the pipeline
=============================
Before launching the pipeline,user should:

1. Decide which containers to use - either docker or singularity **[-with-docker / -with-singularity]**.
2. Fill in both **params.config** and **tools_opt.tsv** files.

To launch the pipeline, please use the following command:

.. code-block:: console

   nextflow run mop_dna.nf -params-file params.yaml  -with-singularity > log.txt


You can run the pipeline in the background adding the nextflow parameter **-bg**:

.. code-block:: console

   nextflow run mop_dna.nf -params-file params.yaml -with-singularity -bg > log.txt

You can change the parameters either by changing **params.config** file or by feeding the parameters via command line:

.. code-block:: console

   nextflow run mop_dna.nf -params-file params.yaml -with-singularity -bg --output test2 > log.txt


You can specify a different working directory with temporary files:

.. code-block:: console

   nextflow run mop_dna.nf -params-file params.yaml -with-singularity -bg -w /path/working_directory > log.txt


Results
====================

Several folders are created by the pipeline within the output directory specified by the **output** parameter:

1.   clair_flow: contains the output of either **clairS** or **clairS-TO**.
2.   sniffles_flow: contains the output of **Sniffles** tool.
3.   filtered_vcf: contains the VCF produced previously that are being filtered.
4.   annotation: contains the VCF produced previously together with annotations produced by **SNPEff** and **ClinVar**