fixed racon-based assembly

Author: vinzenzmay

pixi.lock

@@ -162,6 +162,7 @@ go-shfmt = "*"
 bedtools = "~=2.31"
 minimap2 = "~=2.28"
 lamassemble = "~=1.7.2"
+flye = "~=2.9.6"
 kalign3 = ">=3.4.0"
 pysam = ">=0.23.3,<0.24"
 bcftools = "~=1.20"

pyproject.toml

@@ -95,7 +95,7 @@ def get_parser():
         required=False,
         type=str,
         choices=["lamassemble", "racon"],
-        default="lamassemble",
+        default="racon",
     )
     parser_run_wf.add_argument(
         "--threads", help="number of threads to use", required=True, type=int