mea-pl run-snakefile

Synopsis

mea-pl run-snakefile [OPTIONS] [–debug]

Description

mea-pl run-snakefile runs a snakefile.

Options

--snakefile SNAKEFILE: Path to the snakefile to be executed. (required) If path can be absolute or relative to the current working directory, (eg. ./my_snakefile.smk). If only provided the name of the snakefile (eg. my_snakefile.smk), it will be searched from the rules/ directory of the MEA-Pipeline installation.

-c, --configfile CONFIGFILE: Path to a configuration file in YAML or JSON format. If path can be absolute or relative to the current working directory, (eg. ./my_config.yaml). If only provided the name of the config file (eg. my_config.yaml), it will be searched from the config/ directory of the MEA-Pipeline installation. Multiple config files can be provided by repeating this option.

-t, --targets TARGETS: If not provided, the default target specified in the snakefile will be built. Multiple targets can be provided by repeating this option.

Environment

SNAKEFILE_PROFILE: Directory for Snakemake profile