run

#!/usr/bin/env python
import os
import json
import subprocess

with open("config.json") as conf:
    config = json.load(conf)

snake_out = os.path.join(config['logs'], "snake.out")
snake_err = os.path.join(config['logs'], "snake.err")
stats_path = os.path.join(config['logs'], 'stats.json')

with open(snake_out, 'w') as out, open(snake_err, 'w') as err:
    snake = subprocess.check_call(
        [
            "snakemake",
            "--snakefile", os.path.join(config['src'], 'Snakefile'),
            "--jobscript", os.path.join(config['src'], 'jobscript.sh'),
            "--cluster", 'qsub',
            "--rerun-incomplete",
            "-j", "100",
            "--stats", stats_path,
            "-T",
            "-k",
        ],
        stdout=out, stderr=err
    )