Add missing snpeff option

PathoGenOmics-Lab · Oct 4, 2023 · b02145e · b02145e
1 parent 5ca3f0e
commit b02145e
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/workflow/rules/vaf.smk b/workflow/rules/vaf.smk
@@ -141,8 +141,8 @@ rule variants_effect:
         LOGDIR / "variants_effect" / "log.txt"
     shell:
         """
-        snpeff {params.ref_name} {input.vcf} > {output.ann_vcf}
-        
+        snpeff eff {params.ref_name} {input.vcf} > {output.ann_vcf}
+        rm snpEff_genes.txt snpEff_summary.html
         """
 
 rule vcf_to_tsv: