snakemake-contracts-wrapper 0.4.2

Snakemake rule wrapper that expands named inputs, outputs, and params into script CLI arguments

snakemake-contracts-wrapper

Snakemake rule wrapper that expands named input, output, log, and params objects into script CLI arguments.

Motivation

Snakemake rules commonly repeat the same wiring: --flag {input.foo} --other-flag {output.bar} for every rule that calls a script. This package removes that repetition. It reads the named objects already present on a rule and turns them into ordinary command-line arguments, so the script itself stays unaware of Snakemake and only ever sees CLI flags.

This package is the wrapper layer for snakemake-contracts, but it does not depend on it and can be used on its own.

Usage

As a Python helper:

from snakemake_contracts_wrapper import build_argv, render_shell

argv = build_argv(
    script="scripts/train.py",
    input={"data": "data.csv"},
    output={"model": "model.pkl"},
    params={"epochs": 10},
)
# ["scripts/train.py", "--data", "data.csv", "--output-model", "model.pkl", "--epochs", "10"]

render_shell(
    script="scripts/train.py",
    input={"data": "data.csv"},
    output={"model": "model.pkl"},
)
# "scripts/train.py --data data.csv --output-model model.pkl"

As a Snakemake wrapper, point a rule's wrapper: directive at snakemake_contracts_wrapper.WRAPPER_DIR:

from snakemake_contracts_wrapper import WRAPPER_DIR

rule train:
    input:
        script="scripts/train.py",
        data="data.csv",
    output:
        model="model.pkl",
    params:
        epochs=10,
    wrapper:
        f"file:{WRAPPER_DIR}"

The wrapper requires a named input called script, which is excluded from the generated argument list by default.

Log argument

The Snakemake wrapper does not pass --log unless the rule declares a log: output itself, or the workflow config explicitly opts in with scripts_accept_log_arg: true and a cache path is configured. When both are set and no log: is declared, a default log path is synthesized under {cache}/logs/{script_stem}.log. This opt-in is required because a cache config alone does not prove that every wrapped script accepts a --log CLI argument.

Surface

• build_argv(command, script=None, input=None, output=None, log=None, params=None, exclude_input=("script",), output_prefix="output-")
• render_shell(command, script=None, input=None, output=None, log=None, params=None, exclude_input=("script",), output_prefix="output-")
• namespace_flag(namespace, name, output_prefix="output-")
• snake_to_kebab(name)
• WRAPPER_DIR