Commit 3453c430 authored by MARIJON Pierre's avatar MARIJON Pierre

Add option to set the contig length threshold

parent 9e0b8730
......@@ -20,7 +20,7 @@ rule filter_contigs:
"{prefix}_filtred.fasta"
shell:
"python -m knot.filter_tig {input} {output} -t 100000"
"python -m knot.filter_tig {input} {output} -t " + str(config['min_contig_length'])
rule map_contigs2contigs:
input:
......
......@@ -35,6 +35,8 @@ def main(args = None):
help="read used for assembly")
parser.add_argument("-o", "--output", required=True,
help="output prefix")
parser.add_argument("--contig-min-length", default=100000, type=int,
help="contig with size lower this parameter are ignored")
parser.add_argument("--read-type", choices=["pb", "ont"], default="pb",
help="type of input read, default pb")
parser.add_argument("--help-all", action='store_true',
......@@ -75,7 +77,8 @@ def main(args = None):
"out_prefix="+args["output"],
"contigs_graph="+args["contigs_graph"],
"read_type="+args["read_type"],
"package_path="+package_path,
"min_contig_length="+str(args["contig_min_length"]),
"package_path="+package_path
]
if args["raw_reads"] is not None:
......
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