added default flag for 0 lenth indels

metagenlab · Oct 26, 2024 · 4872558 · 4872558
1 parent 4db4d03
commit 4872558
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/mess/workflow/rules/simulate/short_reads.smk b/mess/workflow/rules/simulate/short_reads.smk
@@ -1,4 +1,4 @@
-art_args = ""
+art_args = "-k 0 "
 if CUSTOM_ERR == None:
     art_args += f"-ss {ERROR} "
 if CUSTOM_ERR:
@@ -16,7 +16,7 @@ if PAIRED:
 
 
 if BAM:
-    art_args += "-sam -M"
+    art_args += "-sam"
 
 
 fq_prefix = os.path.join(dir.out.short, "{sample}", "{fasta}", "{contig}")