--rerun-incomplete in cluster config.yaml not taken as an option in python.py

[jjsanchezgil]

Hi

I tried to set rerun-incomplete: false in the config file but this would not be taken in the execution command. I checked the command constructor in python.py and the --rerun-incomplete option is directly given as default and not parsed as an option above.

    cmd = (
        "snakemake --snakefile {snakefile} --directory {working_dir} "
        "{jobs} --rerun-incomplete "
        "--configfile '{config_file}' --nolock "
        " {profile} --use-conda {conda_prefix} {dryrun} "
        " {target_rule} "
        " {args} "
    ).format(
        snakefile=get_snakefile(),
        working_dir=working_dir,
        jobs="--jobs {}".format(jobs) if jobs is not None else "",
        config_file=config_file,
        profile="" if (profile is None) else "--profile {}".format(profile),
        dryrun="--dryrun" if dryrun else "",
        args=" ".join(snakemake_args),
        target_rule=workflow if workflow!="None" else "",
        conda_prefix= "--conda-prefix "+os.path.join(db_dir,'conda_envs')
    )

I'm aware that the recommendation for cluster execution is to set it as true, but I thought it was good to let you know (just in case I'm not wrong, which is of course very possible) :)