Merge branch 'fix/restrict-calls-to-reference-contigs' of github.com:…

…snakemake-workflows/dna-seq-benchmark into fix/restrict-calls-to-reference-contigs
snakemake-workflows · Sep 12, 2024 · 7d5a91b · 7d5a91b
2 parents 7780a7d + f2e2f33
commit 7d5a91b
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/tools.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: