Add extra

snakemake · Nov 25, 2024 · 54eea00 · 54eea00
1 parent 580e5e2
commit 54eea00
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/bio/sexdeterrmine/wrapper.py b/bio/sexdeterrmine/wrapper.py
@@ -16,15 +16,15 @@
 log = snakemake.log_fmt_shell(
     stdout=False,
     stderr=True,
-    append=True,
+    append=False,
 )
 extra = snakemake.params.get("extra", "")
 
 with TemporaryDirectory() as tempdir:
     old_path = os.getcwd()
     depth_path = os.path.realpath(snakemake.input.depth)
     os.chdir(tempdir)
-    shell(f"sexdeterrmine --Input {depth_path} > out.tsv 2> sexdeterrmine.log")
+    shell(f"sexdeterrmine --Input {depth_path} {extra} > out.tsv 2> sexdeterrmine.log")
 
     log = snakemake.log_fmt_shell(
         stdout=True,