From 4fe2b57d57f469e6004a6d04001540d81b15969f Mon Sep 17 00:00:00 2001
From: jessicaw9910 <jessbwhite@gmail.com>
Date: Fri, 19 Jul 2024 10:35:31 -0400
Subject: [PATCH] changed params.bam directory error (aligned > alignment)

---
 nextflow/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow/main.nf b/nextflow/main.nf
index 5ad3563..0ca9067 100644
--- a/nextflow/main.nf
+++ b/nextflow/main.nf
@@ -20,7 +20,7 @@ params.fastp_json = "${params.outDir}/fastp/*fastp.json"
 params.fastqc_fastq = "${params.outDir}/fastqc/fastq/*/*"
 params.fastqc_fastp = "${params.outDir}/fastqc/fastp/*/*"
 
-params.bam = "${params.outDir}/aligned/*.Aligned.sortedByCoord.out.bam"
+params.bam = "${params.outDir}/alignment/*.Aligned.sortedByCoord.out.bam"
 
 log.info """\
         STAR RNA-Seq NextFlow Pipeline (Reference-Based)