Pyscripts

class snakeboost.SnakemakeArgs(input, output, params, wildcards, threads, resources, log)

Class organizing the data passed from snakemake

This contains all the data, including inputs, outputs, params, etc, passed from the Snakemake rule calling the script.

This class should not be initialized directly, but should be created through the snakemake_args() function

input

Type: List or Dict of paths

output

Type: List or Dict of paths

params

Type: List or Dict of str

wildcards

Type: List or Dict of str

threads

Type: int

resources

Type: List or Dict of str

log

Type: List or Dict of paths

snakeboost.snakemake_args(argv=None, parser=ArgumentParser(prog='__main__.py', usage=None, description=None, formatter_class=<class 'argparse.HelpFormatter'>, conflict_handler='error', add_help=True), input=None, output=None, params=None, wildcards=None, resources=None, log=None)

Snakemake args passed from snakemake rule

Parses the command line call made by Pyscript and returns an instance of SnakemakeArgs for consumption in a python script.

Parameters

argv (optional list[str]) – List of arguments to parse. Uses sys.argv[1:] by default
parser (argparse.ArgumentParser , optional) – Argument parser to use. By default, uses the preconstructed snakemake_args parser. This should be suitable for most applications.

Returns

SnakemakeArgs