From d81b455034b616fbf25915061d891a3e372b1b84 Mon Sep 17 00:00:00 2001
From: phoenixAja <plogan@chanzuckerberg>
Date: Wed, 6 Dec 2023 07:26:36 -0800
Subject: [PATCH] fix to break and sort

---
 workflows/index-generation/index-generation.wdl | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/workflows/index-generation/index-generation.wdl b/workflows/index-generation/index-generation.wdl
index 1255c78d1..5ab18c2b2 100644
--- a/workflows/index-generation/index-generation.wdl
+++ b/workflows/index-generation/index-generation.wdl
@@ -674,8 +674,7 @@ task SplitFastaBySeqLengthAndSort {
         set -euxo pipefail
 
         total_seqs=$(grep ">" ~{fasta} | wc -l)
-        ncbi-compress  \
-            --break-up-fasta-by-sequence-length  \
+        ncbi-compress  break-up-fasta-by-sequence-length  \
             --input-fasta ~{fasta}  \
             --temp-file-output-dir outputs  \
             --total-sequence-count ${total_seqs}  \