Merge pull request #71 from cokelaer/main

add missing dependency on bs4

Author: cokelaer

pyproject.toml

@@ -44,6 +44,7 @@ packages = [
 sequana_lora = "sequana_pipelines.lora.main:main"
 
 [tool.poetry.group.dev.dependencies]
+bs4 = "^4"
 ruff = "^0.0.264"
 pytest = "^7.0.1"
 black = "^23.3.0"

sequana_pipelines/lora/main.py

@@ -241,8 +241,8 @@ def convert(self, value, param, ctx):
         accordingly to '_[12]'.""",
 )
 @click.option(
-    "--reference",
-    "reference",
+    "--reference-file",
+    "reference_file",
     default=None,
     show_default=False,
     type=click.Path(exists=True, file_okay=True),
@@ -270,6 +270,7 @@ def main(**options):
     cfg.input_directory = os.path.abspath(options.input_directory)
     cfg.input_pattern = options.input_pattern
     cfg.input_csv = os.path.abspath(options.input_csv) if options.input_csv else ""
+    cfg.reference_file = os.path.abspath(options.reference_file) if options.reference_file else ""
 
     # prokka
     cfg.prokka.do = True if (options.do_prokka or options.mode == "bacteria") else False