default lamassemble

Author: vinzenzmay

src/svirlpool/__main__.py

@@ -91,11 +91,11 @@ def get_parser():
     )
     parser_run_wf.add_argument(
         "--consensus-method",
-        help="Method for consensus assembly: 'gotoh-msa' (default), 'lamassemble', or 'racon'.",
+        help="Method for consensus assembly: 'gotoh-msa', 'lamassemble' (default), or 'racon'.",
         required=False,
         type=str,
         choices=["lamassemble", "racon", "gotoh-msa"],
-        default="gotoh-msa",
+        default="lamassemble",
     )
     parser_run_wf.add_argument(
         "--threads", help="number of threads to use", required=True, type=int

src/svirlpool/localassembly/consensus.py

@@ -3439,7 +3439,7 @@ def get_consensus_parser(
         type=str,
         choices=["lamassemble", "racon", "gotoh-msa"],
         default="gotoh-msa",
-        help="Method used for consensus assembly: 'gotoh-msa' (default), 'lamassemble', or 'racon'.",
+        help="Method used for consensus assembly: 'gotoh-msa', 'lamassemble' (default), or 'racon'.",
     )
     parser.add_argument(
         "-t", "--threads", type=int, default=1, help="Number of threads to use."

src/svirlpool/workflows/main.smk

@@ -77,7 +77,7 @@ cr_merge_buffer=config["cr_merge_buffer"]
 
 # consensus
 lamassemble_mat = config.get("lamassemble_mat", None)
-consensus_method = config.get("consensus_method", "gotoh-msa")
+consensus_method = config.get("consensus_method", "lamassemble")
 reference_padding_size = config.get("reference_padding_size", 30000)
 
 # min mapq