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
