From 3d24a420f7fa0b84f2eeffc97395fe5da25a7b74 Mon Sep 17 00:00:00 2001
From: DLBPointon <damonlbp@hotmail.co.uk>
Date: Thu, 28 Nov 2024 11:45:34 +0000
Subject: [PATCH] Using realpath so we don't have to pass the bam around like a
 wally

---
 modules/local/generate_samplesheet.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/generate_samplesheet.nf b/modules/local/generate_samplesheet.nf
index 0da00522..3d186677 100644
--- a/modules/local/generate_samplesheet.nf
+++ b/modules/local/generate_samplesheet.nf
@@ -20,7 +20,7 @@ process GENERATE_SAMPLESHEET {
     """
     generate_samplesheet.py \\
         $prefix \\
-        $pacbio_path
+        "\$(realpath $pacbio_path)"
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":