.. _home-page-about:

**************
About the course
**************

.. autosummary::
   :toctree: generated


This slow-paced hands-on course is designed for absolute beginners who want to start using scientific containers to achieve reproducibility of data analysis.

* `Course page <https://github.com/biocorecrg/ropes-linux-mop2-2023>`_


.. |luca| image:: images/lcozzuto.jpg
  :alt: Luca Cozzuto

.. |adelgado| image:: images/adelgado.jpg
  :alt: Anna Delgado

.. |toni| image:: images/thermoso.jpg
  :alt: Toni Hermoso

.. |julia| image:: images/jponomarenko.jpg
  :alt: Julia Ponomarenko



.. list-table:: Main instructors:
   :widths: 50 50 50 50
   :header-rows: 1

   * - Luca Cozzuto
     - Anna Delgado
     - Toni Hermoso
     - Julia Ponomarenko
   * - |luca|
     - |adelgado|
     - |toni|
     - |julia|

.. _home-page-outline:

Outline
============

.. 
        Trainees will work in a dedicated Linux environment.


.. _home-page-learning:

Learning objectives
============

* Learn the basics of command-line Linux
* Locate and fetch Docker/Singularity images from dedicated repositories.
* Execute/Run a Docker/Singularity container from the command line.
* Understand the components of Nextflow pipeline
* Run a Nextflow pipeline using your own data and tuning it with different parameters
* Write a simple Nextflow pipeline.
* Understand the basics of direct RNA sequencing with Nanopore
* Run the different pipelines in Master Of Pores 2 suite. 

Prerequisite / technical requirements
============


Being comfortable working with the CLI (command-line interface) in a Linux-based environment.
Knowledge of containers is not mandatory. The course materials is online in the dedicated GitHub page for self-learning.


Those who follow the course should be able to use a command-line/screen-oriented text editor (such as nano or vi/vim, which are already available in the server) or to be able to use an editor able to connect remotely. For sake of information, below the basics of `nano <https://wiki.gentoo.org/wiki/Nano/Basics_Guide>`_

Having a `GitHub account <https://github.com/join>`_ is recommended.

.. _home-page-dates:

Dates, time, location
============

* Dates: May 15-17, 2023

* Schedule: 09:00-13:00 **CET**

* Location: C/ del Dr. Aiguader, 88, 08003 Barcelona, Spain. Training room, ground floor.

.. _home-page-program:


Program
============


Day 1: Linux Basics
-------------

* 09.00-11:00 Linux basics I
* 11:00-11:30 Coffee break
* 11:30-13:00 Linux basics II

Day 2: Linux containers and Nextflow
-------------

* 09.00-11:00 Containers
* 11:00-11:30 Coffee break
* 11:30-13:00 Nextflow

Day 3: dRNA analysis with Master of Pores 2 
---------------

* 09.00-11:00 Introduction to dRNA sequencing and MoP2
* 11:00-11:30 Coffee break
* 11:30-13:00 MoP2 practical