BIOS4BIOL workflow repository

This repository contains workflows (Snakemake/Nextflow):

• developped by BIOS4BIOL members
• or retrieved from public repository and adapted for our purpose.

Those workflows are available on bioinfo Genotoul core facilities (SGE and/ or SLURM).

Use snakemake on genoclust :

ssh user@genologin.toulouse.inra.fr
module load bioinfo/snakemake-4.5.1
snakemake -s /usr/local/bioinfo/workflows/Snakemake/anApplication/Snakefile \
          --cluster-config /usr/local/bioinfo/workflows/Snakemake/anApplication/ressources_SLURM.yaml \
          --drmaa " -q unlimitq --cpus-per-task={cluster.cpus} --time={cluster.time} --mem={cluster.mem} " --drmaa-log-dir your_slurm_log_dir

To rerun or restart a workflow, simply launch the exact same command.

More info about Snakemake available here

More info about each workflow available into directory Snakemake

Use nextflow on genoclust :

ssh user@genologin.toulouse.inra.fr
module load bioinfo/Nextflow-v0.27.3
nextflow run /usr/local/bioinfo/workflows/Nextflow/anApplication/main.nf -profile genoclust

Rerun/Restart a workflow :

nextflow run /usr/local/bioinfo/workflows/Nextflow/anApplication/main.nf -profile genoclust -resume

More info about Nextflow available here

More info about each workflow available into directory Nextflow

How to add a new workflow in this repository ?

Follow instructions writen in HOWTO.md file.

Who is maintaining this repository ?

• Maria Bernard - maria.bernard@inra.fr -
• Matthieu Charles - Mathieu.charles@inra.fr -
• Sylvain Marthey - sylvain.marthey@inra.fr -
• Céline Noirot - celine.noirot@inra.fr - @cnoirot

Please contact us if you want to participate.