parser.add_argument("-cpus", dest="cpus", help="SLURM --cpus-per-task option.", type=int, default=1) parser.add_argument("-mem", dest="mem", help="SLURM --mem option.", type=int, default=0) # SLURM options args = parser.parse_args() # Input options. seq_run_ids, spec_ids, specs_ordered, spec_abbr, basedirs = globs.get() # Get all the meta info for the species and sequencing runs. if not args.name: name = mcore.getRandStr() else: name = args.name # Get the job name. step = "03-Reformat" prev_step = "02-Decon" # Step vars pad = 26 cwd = os.getcwd() # Job vars
parser.add_argument("-cpus", dest="cpus", help="SLURM --cpus-per-task option.", type=int, default=1) parser.add_argument("-mem", dest="mem", help="SLURM --mem option.", type=int, default=0) # SLURM options args = parser.parse_args() # Input options. seq_run_ids, spec_ids, specs_ordered = globs.get() # Get all the meta info for the species and sequencing runs. if not args.name: name = mcore.getRandStr() else: name = args.name # Get the job name. base_outdir = os.path.abspath("../01-Assembly-data/") assembly_outdir = os.path.join(base_outdir, "05-Scaffolds") assembly_indir = os.path.join(base_outdir, "05-Spades") pad = 26 cwd = os.getcwd() # Job vars