From f31761edd22b895987d7690750ba8647cb261acd Mon Sep 17 00:00:00 2001
From: Nicholas Wiltsie <nwiltsie@mednet.ucla.edu>
Date: Mon, 15 Jul 2024 12:16:12 -0700
Subject: [PATCH] Capitalize SAMtools in output directories

---
 module/annotations.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/module/annotations.nf b/module/annotations.nf
index ebbcb50..018cdfb 100644
--- a/module/annotations.nf
+++ b/module/annotations.nf
@@ -92,7 +92,7 @@ process compress_and_index_HTSlib {
     tuple val(sample_id), path('output.tsv.gz'), path('output.tsv.gz.tbi'), emit: compressed_tsv_with_index
 
     script:
-    intermediate_filepath = "${params.output_dir_base}/samtools-${params.bcftools_version}/intermediate/${task.process}"
+    intermediate_filepath = "${params.output_dir_base}/SAMtools-${params.samtools_version}/intermediate/${task.process}"
 
     slug = "Trinucleotide-${sample_id}"