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.