About the course
This slow-paced hands-on course is designed for absolute beginners who want to start using scientific containers to achieve reproducibility of data analysis.
Luca Cozzuto |
Anna Delgado |
Toni Hermoso |
Julia Ponomarenko |
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Outline
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
Having a GitHub account is recommended.
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.
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