.. _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 6th of February to 9th of February 2024.

* Location: ALBA.

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

* 10:00-11:00 Introduction to Nextflow
* 11:00-11:30 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 Break
* 16:00-17:30 Directive and resuming 

*Day 2: Linux containers*

* 14:00-15:00 - Linux containers. Docker introduction and running
* 15:00-15.30 - Break
* 15:30-17.00 - Building Docker containers. Singularity/Apptainer

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

* 14:00-15:00  Singularity and more processes
* 15:00-15.30  Break
* 15:30-17.00 Profiles and cloud

*Day 4: Nextflow modules and Tower*

* 14:00-15:00 Modules
* 15:00-15.30 Break
* 15:30-17.00 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.

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