fix: add parantheses to catch error log of both commands

Co-authored-by: Johannes Köster <[email protected]>
snakemake-workflows · Sep 12, 2024 · f2e2f33 · f2e2f33
1 parent eb3632d
commit f2e2f33
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/workflow/rules/eval.smk b/workflow/rules/eval.smk
@@ -118,8 +118,8 @@ rule restrict_to_reference_contigs:
     conda:
         "../envs/bcftools.yaml"
     shell:
-        "bcftools view --regions $(cut -f1 {input.ref_index} | tr '\\n' ',') {input.calls} | "
-        "bcftools reheader -f {input.ref_index} > {output} 2> {log}"
+        "(bcftools view --regions $(cut -f1 {input.ref_index} | tr '\\n' ',') {input.calls} |"
+        " bcftools reheader -f {input.ref_index} > {output}) 2> {log}"
 
 
 rule normalize_calls: