Usage

A dry-run (always a good idea before each execution)

(phap)$ snakemake -n \
--use-conda \
--conda-frontend mamba \
--use-singularity \
--singularity-args "-B path/to/vhmnet/data:/data -B path/to/crisporopendb/data:/data2 -B path/to/phist/data:/data3"

Basic

# From within this directory
# Make sure you have defined a samplesheet
(phap)$ snakemake -p \
--use-conda \
--conda-frontend mamba \
--use-singularity -j16 \
--singularity-args "-B path/to/vhmnet/data:/data -B path/to/crisporopendb/data:/data2 -B path/to/phist/data:/data3"

where /path/to/<TOOL>/data are directories containing the databases for the different tools as explained in the Installation section.

  • The -j flag controls the number of jobs (cores) to be run in parallel. Change this according to your setup.

  • The -p flag prints commands that are being submitted for execution.

  • Binding the data dir with the --signularity-args is required. You must also provide this path as a value for the data_dir option in the config.yaml.

Advanced

For more complex use cases (e.g. executing some intermediate step again without affecting the rest of the output) it is wise to check snakemake’s help menu with

$ snakemake --help

Daunting at first, but covers a lot.