<commit_before>import os,sys,string,subprocess
import argparse

parser = argparse.ArgumentParser(description='snakemake and metacompass params')
parser.add_argument("-t",'--threads', type=int,help='num threads',default=1, nargs='?')
parser.add_argument("-i",'--iterations', type=int, help='num iterations',default=1, nargs='?')
parser.add_argument("-u",'--unlock', type=bool, help='unlock',default=False, nargs='?')
parser.add_argument("-r",'--ref', help='reference genome',default="",nargs='?')
parser.add_argument("-s",'--snakefile', help='snakemake file',default="",nargs='?',required=1)
#parser.add_argument("-I",'--SampleIds', help='sample ids',default="", nargs='*',required=1)
parser.add_argument("-S",'--Samples', help='Provide file with fq reads (1 file per line)',default="", nargs='?',required=1)
parser.add_argument("-q",'--qsub', help='',default="", nargs='?',required=1)
parser.add_argument("-c",'--config', help='config (json) file',default="",nargs='?',required=1)
parser.add_argument("-F",'--force', help='force snakemake to rerun',type=bool, default="False",nargs='?',required=1)
parser.add_argument("-v",'--verbose', help='verbose',type=bool, default="False",nargs='?',required=1)



args = parser.parse_args()
unlock = args.unlock
threads = int(args.threads)
iterations = args.iterations
ref = args.ref
snakefile = args.snakefile
config = args.config
samples = args.Samples.replace(" ","")
qsub = args.qsub
force = args.force
verbose = args.verbose

if force:
   if os.path.exists("Sample1.fasta"):
      os.system("rm Sample1.fasta")
   if os.path.exists("Sample1.marker.match.1.fastq"):<commit_msg>qsub not required<commit_after>import os,sys,string,subprocess
import argparse

parser = argparse.ArgumentParser(description='snakemake and metacompass params')
parser.add_argument("-t",'--threads', type=int,help='num threads',default=1, nargs='?')
parser.add_argument("-i",'--iterations', type=int, help='num iterations',default=1, nargs='?')
parser.add_argument("-u",'--unlock', type=bool, help='unlock',default=False, nargs='?')
parser.add_argument("-r",'--ref', help='reference genome',default="",nargs='?')
parser.add_argument("-s",'--snakefile', help='snakemake file',default="",nargs='?',required=1)
#parser.add_argument("-I",'--SampleIds', help='sample ids',default="", nargs='*',required=1)
parser.add_argument("-S",'--Samples', help='Provide file with fq reads (1 file per line)',default="", nargs='?',required=1)
parser.add_argument("-q",'--qsub', help='',default="", nargs='?',required=0)
parser.add_argument("-c",'--config', help='config (json) file',default="",nargs='?',required=1)
parser.add_argument("-F",'--force', help='force snakemake to rerun',type=bool, default="False",nargs='?',required=1)
parser.add_argument("-v",'--verbose', help='verbose',type=bool, default="False",nargs='?',required=1)



args = parser.parse_args()
unlock = args.unlock
threads = int(args.threads)
iterations = args.iterations
ref = args.ref
snakefile = args.snakefile
config = args.config
samples = args.Samples.replace(" ","")
qsub = args.qsub
force = args.force
verbose = args.verbose

if force:
   if os.path.exists("Sample1.fasta"):
      os.system("rm Sample1.fasta")
   if os.path.exists("Sample1.marker.match.1.fastq"):
{'fraction_non_alphanumeric': 0.2219482120838471, 'fraction_numerical': 0.008631319358816275, 'mean_word_length': 7.653333333333333, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5295811', 'n_tokens_mistral': 1110, 'n_tokens_neox': 1123, 'n_words': 179}