How to run a nf-core nextflow workflow on genotoul ?

How to run a nf-core nextflow workflow on genotoul ? (14/10/2021)

This training session is organized by the Genotoul bioinfo platform and aims at learning nf-core workflow submission, error understanding and resuming jobs. We will present :

  • the Nextflow software
  • the nf-core community and pipelines
  • What is a singularity image ?
  • Where are installed the nf-core workflows ? Which version do I use ?
  • How to run a workflow and which config file is used ?
  • Which kind of error I can get ?
  • How to reproduce error to understand the problem ?
  • How to resume failed jobs?
  • How to handle genome indexes ?
  • How to monitor my process and then well configure my workflow ?

This is NOT a bioinformatic training on a particular workflow or a training on how to develop a workflow.



This training is focused on practice. It consists of several modules with a large variety of exercises:

  • Start at 09:00 am
  • End at 17:00 pm


The session will take place in the room ‘salle de formation’ at INRAE center of Toulouse-Auzeville.


Prerequisites: Ability to use a Linux environment and SLURM (see Linux training and Cluster training). Training materials will be available on the website before the session. Slides in a “taking notes” format will be downloadable from our web site. A Unix reference command leaflet will also be provided. Only the latter will be available during the session.



Training material: tutorial



Bookings: How to run a nf-core nextflow workflow on genotoul ?

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