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, Snakemake currently defaults to mamba as conda frontend. Please be aware that for that to work one should follow the recommendations at MAMBA. However, using conda-libmamba-solver, the conda frontend can lead to an even better and more stable experience. We currently recommend to set a fixed directory to store environments (here conda_envs) and run the conda frontend.

--conda-frontend conda --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.