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.