Getting started with Snakemake
About this course
Targeted audience:
- bioinformaticians
- biologists that have experience in running scripts or programmes through command lines
- An introduction to Snakemake and on why to use workflow tools
- Example exercises to get familiar with Snakemake
Requirements:
- know a minimum of bash/shell or other programming language
- bring your own laptop with a possibility of connecting to the internet on the Gif CNRS campus (Eduroam for example)
- have an I2BC account/email address (https://multipass.i2bc.paris-saclay.fr/)
- have access & know how to connect and use the I2BC cluster (I2BC cluster training)
If you have routine bioinformatics analyses requiring a series of different tools, this training course is made for you!
Perhaps you’ve already heard of Nextflow and/or Snakemake? These are popular bioinformatics workflow managers designed to minimise the number of manual steps in your analyses. They help you automate, monitor and scale up your analysis pipelines (to the I2BC computing cluster, for example).
In this course, we will introduce you to Snakemake and help you take your first steps using small, simple examples. Of course, feel free to bring along your own analysis pipelines if you wish.
Course organisers:
Emilie Drouineau (GENOMES/REMOD),
Fadwa El-Khaddar (PF/BIOI2, GENOMES/SSFA, GENOMES/BIM),
Chloé Quignot (PF/BIOI2 – ORCID: 0000-0001-8504-232X),
Claire Toffano-Nioche (GENOMES/SSFA – ORCID: 0000-0003-4134-6844)
Contacts for help:
Don’t hesitate to contact the course organisers by email (they all have I2BC addresses).
We also encourage you to join the BIOI2 group on FramaTeam (just create an account with your I2BC email address first, then click on the link), and to post your questions in the Snakemake channel.