Run on Slurm

Snakemake

You can either use the slurm profile adapted from Snakemake-Profiles that comes with this repository, or go through the process of manually creating one, either using the cookiecutter example in the Snakemake-Profiles repository or on your own. You can also adapt the example that comes with this repository and execute

monsda -j ${cpus} --configfile ${config.json} --directory ${PWD} --profile ${path_to_slurm_profile}

Further adaptions like grouping of jobs and advanced configs for rule based performance increase will be tackled in future releases of MONSDA.

Nextflow

Cluster config for Nextflow follows the description Nextflow-Executors and Nextflow-Profiles. To use SLURM as executor you can adapt the profile that comes with this repository and simply append

export NXF_EXECUTOR=slurm

to the call to MONSDA.