caput.pipeline.runner

Command-line interface and helper functions for running pipelines.

This module contains functions to run and queue pipelines, along with a command line interface (CLI) for user interaction.

Basic Functions

These functions just act as convenience wrappers around the core pipeline management functionality.

• run_pipeline()

• template_run()

• lint_config()

Cluster Functions

These are additional functions to support running pipelines on compute clusters using job schedulers like SLURM or PBS.

• queue()

• template_queue()

• register_system()

Functions

lint_config(→ None)	Lint a pipeline config file without running it.
queue(configfile[, submit, lint, profile, profiler, ...])	Queue a pipeline on a cluster from the given configfile.
register_system(→ None)	Register new queue system(s) from a TOML file.
run_pipeline(→ None)	Run a pipeline immediately from the given configfile.
template_queue(templatefile, var, overwrite[, ...])	Queue a pipeline from the given templatefile.
template_run(→ None)	Run a pipeline from the given templatefile.