ssusearch

#!/usr/bin/env python
"""
Execution script for snakemake workflows.
"""
import argparse
import os.path
import sys
import pprint
import subprocess

__version__ = '1.0.0'

thisdir = os.path.realpath(os.path.dirname(__file__))

def main(args, unknown):
    # first, find the Snakefile
    snakefile = None
    if os.path.exists(args.snakefile) and not os.path.isdir(args.snakefile):
        snakefile = args.snakefile
    else:
        snakefile = os.path.join(thisdir, 'Snakefile')
        if not os.path.exists(snakefile):
            sys.stderr.write('Error: cannot find Snakefile at {}\n'.format(snakefile))
            sys.exit(-1)

    snakefile = os.path.abspath(snakefile)
    # next, find the workflow configfile, a.k.a config.yaml
    configfile = None
    if os.path.exists(args.configfile) and not os.path.isdir(args.configfile):
        configfile = args.configfile
    else:
        for suffix in ('', '.yaml', 'yml'):
            tryfile = os.path.join(thisdir, args.configfile + suffix)
            if os.path.exists(tryfile) and not os.path.isdir(tryfile):
                sys.stderr.write('Found configfile at {}\n'.format(tryfile))
                configfile = tryfile
                break

    if not configfile:
        sys.stderr.write('Error: cannot find paramsfile {}\n'.format(args.paramsfile))
        sys.exit(-1)

    configfile = os.path.abspath(configfile)

    print('--------')
    print('Details:')
    print('\tsnakefile: {}'.format(snakefile))
    print('\tconfigfile: {}'.format(configfile))
    print('--------')

    if args.dryrun:
        arg_list = ['snakemake', '--use-conda', '--snakefile', snakefile, '--configfile', configfile, '--dryrun']
    else:
        arg_list = ['snakemake', '--use-conda', '--snakefile', snakefile, '--configfile', configfile]
    arg_list = arg_list + unknown
    # run!!
    status = subprocess.call(arg_list)
    return status

if __name__ == '__main__':
    parser = argparse.ArgumentParser(
            description='Run snakemake workflows using the given config file & metadata file.', 
            usage="""
*** ssusearch --snakefile <Snakefile> --configfile <config.yaml> [other snakemake params]
*** All snakemake options are allowed. See details in snakemake help.
            """
    )

    parser.add_argument('-s', '--snakefile', default='Snakefile', help='default: %(default)s')
    parser.add_argument('--configfile', default='config.yaml', help='default: %(default)s')
    parser.add_argument('-n', '--dryrun', action='store_true', help='check workflow without actually running')
    parser.add_argument('-v', '--version', action='version', version='{version}'.format(version=__version__))
    args, unknown = parser.parse_known_args()

    sys.exit(main(args, unknown))