Document that onstart is recommended to be used

[nh13]

If there is any code prior to running the rules that creates directories, they may not have the correct paths. This is because snakeparse needs to "source" the snakefile prior to actually running it, and doing so without the parsed pipeline arguments.

For example:

from snakeparse.parser import argparser
from pathlib import Path

def snakeparser(**kwargs):
    p = argparser(**kwargs)
    p.parser.add_argument('-o', '--output-dir',        help='The output directory.', default=Path('.'), type=Path)
    return p

args = snakeparser().parse_config(config=config)

args.output_dir.mkdir(parents=True, exist_ok=True)

rule all:
   str(args.output_dir / "dummy.txt")

rule dummy:
   output: str(args.output_dir / "dummy.txt"
   shell: """echo Hi > {output}"""

This should be instead:

from snakeparse.parser import argparser
from pathlib import Path

def snakeparser(**kwargs):
    p = argparser(**kwargs)
    p.parser.add_argument('-o', '--output-dir',        help='The output directory.', default=Path('.'), type=Path)
    return p

args = snakeparser().parse_config(config=config)

onstart:
   args.output_dir.mkdir(parents=True, exist_ok=True)

rule all:
   str(args.output_dir / "dummy.txt")

rule dummy:
   output: str(args.output_dir / "dummy.txt"
   shell: """echo Hi > {output}"""