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Nextflow
Snakemake
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HOWTO.md
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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 ?

Please contact us if you want to participate.