ngs-pl

Synopsis

ngs-pl [-h] [-i] [-l]

ngs-pl COMMAND [OPTIONS] [–debug]

Description

ngs-pl is the front end to execute all NGS-Pipeline commands.

Options

-h, --help: Show this help message and exit.

-i: Run in interactive mode, using IPython shell.

-l, --list: List all available commands and exit.

--debug: Enable debug mode for detailed logging.

Environment

NGSENV_BASEDIR: Path to the NGS-Pipeline base environment directory.

NGS_PROMPT: Prompt string to show in shell.

NGS_PIPELINE_BASE: Path to the NGS-Pipeline repository directory.

NGS_PIPELINE_LOGLEVEL: Set the logging level, with numeric values.

NGS_PIPELINE_CMD_MODS: Colon-separated list of additional directories to search for command modules.

SNAKEMAKE_PROFILE: Path to the Snakemake profile directory.