From 032a92ec7401e01f93defbbf8803d6531e6bf6c5 Mon Sep 17 00:00:00 2001
From: jvfe <jvfecav@gmail.com>
Date: Fri, 19 Apr 2024 13:15:46 -0300
Subject: [PATCH] hotfix: Add check in unmapped for single_end

Signed-off-by: jvfe <jvfecav@gmail.com>
---
 modules/local/samtools_unmapped.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/local/samtools_unmapped.nf b/modules/local/samtools_unmapped.nf
index 9a34bca..a35e6cd 100644
--- a/modules/local/samtools_unmapped.nf
+++ b/modules/local/samtools_unmapped.nf
@@ -19,9 +19,9 @@ process SAMTOOLS_UNMAPPED_PAIRS {
     script:
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
-
+    def format = meta.single_end ? "4" : "12"
     """
-     samtools view -b -f 12 -F 256 \\
+     samtools view -b -f $format -F 256 \\
         $input \\
         > ${prefix}.bam