How to run a nf-core nextflow workflow on genotoul ? (12/11/2024)
This training session is organized by the Genotoul bioinfo platform and aims at learning nf-core workflow submission, error understanding, resuming jobs and ressource reservation. We will present and practice:
- 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 resume failed jobs?
- How to handle genome indexes ?
- How to monitor my process and then well configure my workflow ?
- How do you best adjust CPU and RAM reservations?
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 up to dat will be available below before the session.
Training material: tutorial