.. _home-page-about:

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

.. autosummary::
   :toctree: generated


This slow-paced hands-on internal course is designed for absolute beginners who want to start using  `Nextflow DSL2 <https://www.nextflow.io>`_ to achieve reproducibility of the data analysis.


.. |luca| image:: images/lcozzuto.jpg
  :alt: Alternative text

.. |toni| image:: images/thermoso.jpg
  :alt: Alternative text
  

.. |julia| image:: images/jponomarenko.jpg
  :alt: Alternative text



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

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


.. _home-page-dates

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

* Dates: From 12th of September to 15th of September 2023.
* Time: 12/09/23         9:30 - 17:00h (CET)
* Time: 13-14-15 09/23   9:30 - 13:00h (CET)

* Location: Training room, CRG.

Program
------------------------
  
*Day 1: Understand and run a basic Nexflow pipeline*

* 09:30-11:00 Introduction to Nextflow
* 11:00-11:30 Coffee break
* 11:30-13:00 Making simple scripts: channels operators and workflows

*Day 1: Write, modify, and run a complex pipeline*

* 14:30-15:30 More complex scripts
* 15:30-16:00 Coffee break
* 16:00-17:00 Directive and resuming 

*Day 2: Linux containers*

* 09:30-11:00 - Linux containers: Docker & Singularity/Apptainer
* 11:00-11.30 - Coffee break
* 11:30-13.00 - Decoupling resources, parameters and main script

*Day 3: Run a Nextflow pipeline in different environments*

* 09:30-11:00 Singularity and more processes
* 11:00-11:30 Coffee break
* 11:30-13:00 Profiles and cloud

*Day 4: Nextflow modules and Tower*

* 09:30-11:00 Modules
* 11:00-11:30 Coffee break
* 11:30-13:00 Tower


.. _home-page-outline:

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

This Nextflow course will train participants to build Nextflow pipelines and run them with Linux containers.

.. _home-page-learning:

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

* Execute/Run a Nextflow pipeline.
* Describe and explain Nextflow basic concepts.
* Test and modify a Nextflow pipeline.
* Implement short blocks of code into a Nextflow pipeline.
* Understand, run and build Linux containers
* Use containers in Nextflow processes
* Develop a Nextflow pipeline from scratch.
* Run a pipeline in diverse computational environments (local, HPC, cloud).
* Share a pipeline.

.. _home-page-prereq:

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.

Practitioners will need to connect during the course to a remote server via the "ssh" protocotol. You can learn about it `here <https://www.hostinger.com/tutorials/ssh-tutorial-how-does-ssh-work>`_

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.