Chap I. Nextflow tutorial for Genotoul

In this chapter you will learn how to use nextflow.

Set up the genotoul environement

• Log on genologin

  ssh -X <username>@genologin.toulouse.inrae.fr
  

• Create tutorial working directory and log in a node

  cd work
  mkdir nextflow-tutorial
  cd nextflow-tutorial
  srun --mem 4G --pty bash
  

• Creates Nextflow directories

  This step has to be done only one time and set up the home directories for nextflow and singularity as on genotoul home dir is limited to 100Mo!

On genologin execute once the following script which creates two directories : ~/work/.nextflow and ~/work/.singularity and creates symbolic link in home directory.

sh /usr/local/bioinfo/src/NextflowWorkflows/create_nfx_dirs.sh

• Load modules

On genologin server, each time you'll want to use Nextflow you have to load module. Search the available Nextflow modules and load the last version.

search_module nextflow
module load bioinfo/Nextflow-v20.10.0

Tip: to get short help on Nextflow command you can use tldr

module load system/Python-3.6.3
tldr nextflow