From f20e30b95c76a9a79aaf3284be17c739b12e5209 Mon Sep 17 00:00:00 2001
From: William Harvey <wharvey@uw.edu>
Date: Wed, 28 Feb 2024 14:42:55 -0800
Subject: [PATCH] Sort final bed

---
 pipelines/summarize_flagger_output/workflow/Snakefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pipelines/summarize_flagger_output/workflow/Snakefile b/pipelines/summarize_flagger_output/workflow/Snakefile
index d0ac92e..e8ebc1b 100644
--- a/pipelines/summarize_flagger_output/workflow/Snakefile
+++ b/pipelines/summarize_flagger_output/workflow/Snakefile
@@ -123,7 +123,7 @@ rule liftover_bed:
         hrs=2,
     shell:
         """
-        cut -f 1,3,4,13 {input.paf} | sed 's/id:Z://' | sed 's/_TO.*//' | awk '{{if (NF == 4) print}}' > {output.bed}
+        cut -f 1,3,4,13 {input.paf} | sed 's/id:Z://' | sed 's/_TO.*//' | awk '{{if (NF == 4) print}}' | sort -k1,1 -k2,2n > {output.bed}
         """