Start a pipline run

Snakemake

Activate the MONSDA conda environment and run

monsda --help

to see the help and available options that will be passed through to Snakemake.

To start a job with Snakemake, which is the default, run

monsda -j NUMBER_OF_CORES -c YOUR_CONFIG.json --directory ${PWD}

or add additional arguments for Snakemake as you see fit, we highly recommend to set mamba as conda frontend and set a fixed directory to store environments (here conda_envs)

--conda-frontend mamba --conda-prefix path_to_conda_envs

Nextflow

To run MONSDA in Nextflow mode just add ‘–Nextflow’

monsda --Nextflow -j NUMBER_OF_CORES -c YOUR_CONFIG.json --directory ${PWD}

As with Snakemake additional arguments for Nextflow can be added and will be passed through.