Snakefile

# import 
from __future__ import print_function
import os
import sys
import re
import glob
import socket
import getpass
import subprocess
from distutils.spawn import find_executable
import pandas as pd

# load
configfile: 'config.yaml'

# general functions
def ssw(x, *args, **kwargs):
    sys.stderr.write(x, *args, **kwargs)

# setup
## pipeline utils
snake_dir = config['pipeline']['snakemake_folder']
include: snake_dir + 'bin/ll_pipeline_utils/Snakefile'
config_default(config, 'pipeline', 'name')
## custom functions
def make_fasta_splits(n_jobs, zero_pad=3):
    if str(n_jobs).lstrip().startswith('Skip'):
        n_jobs = 1
    zero_pad = '{0:0' + str(zero_pad) + 'd}'
    return [str(zero_pad.format(x+1)) for x in range(n_jobs)]

# setting paths
config['samples_file'] = os.path.abspath(config['samples_file'])
config['pipeline']['snakemake_folder'] = \
    os.path.abspath(config['pipeline']['snakemake_folder']) + '/'

# uniref
config['uniref_name'] = str(config['uniref_name']).rstrip().lower()
if config['uniref_name'] == 'uniref50':
    config['uniref_other_name'] = 'uniref90'
elif config['uniref_name'] == 'uniref90':
    config['uniref_other_name'] = 'uniref50'
else:
    msg = 'Only "uniref90" and "uniref50" supported for "uniref_name:". Value provided: {}'
    raise ValueError(msg.format(config['uniref_name']))

## base of the snakefile hierarchy 
include: snake_dir + 'bin/Snakefile'
include: snake_dir + 'bin/utils/Snakefile'

## pipeline main
wildcard_constraints:
    sample="[^/]+",
    uniref="[^/]+"

localrules: all

rule all:
    input:
        all_which_input