Fix sambamba filter rule to use new API

cokelaer · Sep 20, 2022 · 9560280 · 9560280
1 parent 178ce5c
commit 9560280
Showing 1 changed file with 1 addition and 2 deletions.
diff --git a/sequana_pipelines/variant_calling/variant_calling.rules b/sequana_pipelines/variant_calling/variant_calling.rules
@@ -197,8 +197,7 @@ if config["sambamba_filter"]["do"]:
         output:
             "{sample}/sambamba_filter/{sample}.filter.sorted.bam"
         log:
-            out="{sample}/sambamba_filter/{sample}_sambamba_filter.out",
-            err="{sample}/sambamba_filter/{sample}_sambamba_filter.err"
+            "{sample}/sambamba_filter/{sample}_sambamba_filter.log",
         params:
             threshold=config["sambamba_filter"]["threshold"],
             options=config["sambamba_filter"]["options"]