From cc31d59a4d080fde3c9f64a151d7332231f21d99 Mon Sep 17 00:00:00 2001
From: lkress <35309241+LKress@users.noreply.github.com>
Date: Fri, 19 Jul 2024 09:55:30 +0000
Subject: [PATCH] Removed outSAMtype parameter

---
 modules/02_star.nf | 2 --
 1 file changed, 2 deletions(-)

diff --git a/modules/02_star.nf b/modules/02_star.nf
index f06d9b1..2f74fd0 100644
--- a/modules/02_star.nf
+++ b/modules/02_star.nf
@@ -28,7 +28,6 @@ process STAR {
     --outReadsUnmapped Fastx \
     --outFilterMismatchNoverLmax 0.02 \
     --runThreadN ${task.cpus} \
-    --outSAMtype BAM SortedByCoordinate \
     --outFileNamePrefix ${name}.
 
     mv ${name}.Aligned.sortedByCoord.out.bam ${name}.bam
@@ -67,7 +66,6 @@ process STAR_SE {
     --outReadsUnmapped Fastx \
     --outFilterMismatchNoverLmax 0.02 \
     --runThreadN ${task.cpus} \
-    --outSAMtype BAM SortedByCoordinate \
     --outFileNamePrefix ${name}.
 
     mv ${name}.Aligned.sortedByCoord.out.bam ${name}.bam