From 43bac2f80554af794b1f7c5609c68870e067fdab Mon Sep 17 00:00:00 2001
From: farchaab <farid.chaabane@chuv.ch>
Date: Fri, 3 Nov 2023 12:41:43 +0100
Subject: [PATCH] use "--" with snakemake args

---
 assembly_finder/assembly_finder.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/assembly_finder/assembly_finder.py b/assembly_finder/assembly_finder.py
index 8245f84..44723c1 100644
--- a/assembly_finder/assembly_finder.py
+++ b/assembly_finder/assembly_finder.py
@@ -49,7 +49,10 @@ def get_snakefile():
 
       github: https://github.com/metagenlab/assembly_finder
       """
-CONTEXT_SETTINGS = dict(help_option_names=["-h", "--help"])
+CONTEXT_SETTINGS = {
+    "help_option_names": ["-h", "--help"],
+    "ignore_unknown_options": True,
+}
 
 
 @click.command(help=desc, context_settings=CONTEXT_SETTINGS)
@@ -212,7 +215,7 @@ def cli(
         dryrun = ""
 
     if snakemake_args:
-        args = " ".join(["--" + arg for arg in snakemake_args])
+        args = " ".join([arg for arg in snakemake_args])
     else:
         args = ""