From cf982a7e5ff39df52224d567774092ac6f3cdf46 Mon Sep 17 00:00:00 2001
From: ens-ftricomi <ftricomi@ebi.ac.uk>
Date: Thu, 15 Aug 2024 17:20:18 +0100
Subject: [PATCH] bug fix genomeDirPath

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

diff --git a/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf b/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf
index c3ab961..afdd92c 100644
--- a/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf
+++ b/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf
@@ -39,7 +39,7 @@ process INDEX_GENOME {
     //if (!genomeIndexFile.exists() || genomeIndexFile.length() == 0) {
     // Read the .fna file and perfor
     // d= new File("${genomeDir}")
-    def genomefilePath=d.listFiles().find { it.name.endsWith('.fna') }
+    def genomefilePath=genomeDirPath.listFiles().find { it.name.endsWith('.fna') }
     def genomeFile=genomefilePath.absolutePath
     // Function to calculate the min value
     def min = { a, b -> a < b ? a : b }