diff --git a/pipelines/nextflow/modules/star_alignment/index_genome.nf b/pipelines/nextflow/modules/star_alignment/index_genome.nf
index 0975544..7ae725b 100644
--- a/pipelines/nextflow/modules/star_alignment/index_genome.nf
+++ b/pipelines/nextflow/modules/star_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("${genomeDir}")
-    def genomefilePath=d.listFiles().find { it.name.endsWith('.fna') }
+    def genomefilePath=genomeDirPath.listFiles().find { it.name.endsWith('.fna') }
     def genomeFile=genomefilePath.absolutePath
     // Function to calculate the min value
     def min = { a, b -> a < b ? a : b }
diff --git a/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf b/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf
index 45ddebc..36a1651 100644
--- a/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf
+++ b/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf
@@ -39,7 +39,7 @@ process INDEX_GENOME {
     //if (!genomeIndexFile.exists() || genomeIndexFile.length() == 0) {
     // Read the .fna file and perfor
     // d= new File("${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 }