diff --git a/src/nf_modules/bowtie2/main.nf b/src/nf_modules/bowtie2/main.nf
index d96b12140838a50ba1914d18535f6d322ed0b4a1..e17e7f2448e1c15271fad4aa9f1e954eae2498bc 100644
--- a/src/nf_modules/bowtie2/main.nf
+++ b/src/nf_modules/bowtie2/main.nf
@@ -35,8 +35,8 @@ process mapping_fastq_pairedend {
   publishDir "results/mapping/bams/", mode: 'copy'
 
   input:
+  path index
   tuple val(pair_id), path(reads)
-  path index.collect()
 
   output:
   tuple val(pair_id), path("*.bam"), emit: bam
@@ -74,8 +74,8 @@ process mapping_fastq_singleend {
   publishDir "results/mapping/bams/", mode: 'copy'
 
   input:
+  path index
   tuple val(file_id), path(reads)
-  path index.collect()
 
   output:
   set file_id, "*.bam", emit: bam
diff --git a/src/nf_modules/kallisto/main.nf b/src/nf_modules/kallisto/main.nf
index a2dc3d707e8a372f6dd1644a0f1f64954a19b18e..5b0a150f210fb4d8451eaf7715bb14779ea2c277 100644
--- a/src/nf_modules/kallisto/main.nf
+++ b/src/nf_modules/kallisto/main.nf
@@ -29,8 +29,8 @@ process mapping_fastq_pairedend {
   publishDir "results/mapping/counts/", mode: 'copy'
 
   input:
+  path index
   tuple val(pair_id), path(reads)
-  path index.collect()
 
   output:
   path "${pair_id}", emit: counts
@@ -53,8 +53,8 @@ process mapping_fastq_singleend {
   publishDir "results/mapping/counts/", mode: 'copy'
 
   input:
+  path index
   tuple val(file_id), path(reads)
-  path index.collect()
 
   output:
   path "${pair_id}", emit: counts