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.