.. _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 `Nextflow DSL2 `_ to achieve reproducibility of the data analysis. * `Course page `_ .. |luca| image:: images/lcozzuto.jpg :alt: Alternative text .. |toni| image:: images/thermoso.jpg :alt: Alternative text .. |jespi| image:: images/jespinosa.jpg :alt: Alternative text .. |julia| image:: images/jponomarenko.jpg :alt: Alternative text .. list-table:: Main instructors: :widths: 50 50 50 50 :header-rows: 1 * - Luca Cozzuto - Toni Hermoso - Jose Espinosa-Carrasco - Julia Ponomarenko * - |luca| - |toni| - |jespi| - |julia| .. _home-page-outline: Outline ============ This Linux Containers and Nextflow course will train participants to build Nextflow pipelines and run them with `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 `_ platform. The link will be provided via the `CRG learning platform `_. .. Trainees will work in a dedicated `AWS environment `_. .. _home-page-learning: Learning objectives ============ * Locate and fetch Docker/Singularity images from dedicated repositories. * Execute/Run a Docker/Singularity container from the command line. * 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 `_ 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 `_ Having a `GitHub account `_ is recommended. .. _home-page-dates: Dates, time, location ============ * Dates: Monday May 30 - Friday June 3, 2022. Tuesday June 7, 2022 * 9:30 - 13:30 **CET** * Location: virtual, via Zoom. .. _home-page-program: Suggested program ============ .. _home-page-day1: Day 1: Introduction to Linux containers and Docker (May 30) ------------- * 09:30-11:00 Introduction to containers and Docker * 11:00-11:30 Break * 11:30-13:30 Docker .. _home-page-day2: Day 2: Docker and Singularity (May 31) ------------- * 09:30-11:00 More advanced Docker * 11:00-11:30 Coffee break * 11:30-13:30 Singularity .. _home-page-day3: Day 3: Understand and run a basic Nexflow pipeline (June 1) ------------- * 09:30-11:00 Introduction to Nextflow * 11:00-11:30 Coffee break * 11:30-13:30 Making simple scripts .. _home-page-day4: Day 4: Write, modify and run a complex pipeline (June 2) ------------- * 09:30-11:00 Decoupling params, resources and main script * 11:00-11:30 Coffee break * 11:30-13:30 Using public pipelines .. _home-page-day5: Day 5: Run a Nextflow pipeline in different environments, share and report (June 3) ------------- * 09:30-11:00 Profiles and cloud * 11:00-11:30 Coffee break * 11:30-13:30 Modules and Tower .. _home-page-day6: Day 6: nf-core (June 7) ------------- * 09:30-10:30 Introduction to nf-core (TBC) * 10:30-11:00 nf-core for users I (TBC) * 11:00-11:30 Coffee break (TBC) * 11:30-12:30 nf-core for users II (TBC) * 12:30-13:30 nf-core for developers (TBC)