.. _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.

* `Course page <https://www.crg.eu/en/event/coursescrg-reproducible-research-and-data-analysis-using-containers-nextflow-2022>`_


.. |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-outline:

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

This Linux Containers and Nextflow course will train participants to build Nextflow pipelines and run them with `Singularity <https://sylabs.io/singularity/>`_ containers.

It is designed to provide trainees with short and frequent hands-on sessions, while keeping theoretical sessions to a minimum.

The course will be fully virtual via the `Zoom <https://zoom.us/>`_ platform. The link will be provided via the `CRG learning platform <https://moodle.crg.eu/>`_.

.. 
        Trainees will work in a dedicated `AWS environment <https://en.wikipedia.org/wiki/AWS/>`_.


.. _home-page-learning:

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

* Locate and fetch Nextflow pipelines from dedicated repositories.
* 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.
* 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.

.. _home-page-dates:

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

* Dates: Jun 30 - July 1, 2022.

* 9:30 - 17:00 **CET**


* Location: CRG training room.

.. _home-page-program:


Suggested program
============


.. _nextflow_1-page:

Day 1: Understand and run a basic Nexflow pipeline (June 30)
-------------

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

.. _nextflow_2-page:

Day 1: Write, modify and run a complex pipeline (Jun 30)
-------------

* 14:30-15:30 More complex scripts: Directive and resuming
* 15:30-16:00 Coffee break
* 16:00-17:00 Decoupling resources, parameters and main script



.. _nextflow_3-page:

Day 2: Run a Nextflow pipeline in different environments (Jul 1)
-------------

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

.. _nextflow_4-page:

Day 2: Nextflow modules and Tower
-------------

* 14:30-15:30 Modules
* 15:30-16:00 Coffee break
* 16:00-17:00 Tower