diff --git a/src/nf_modules/bedtools/main.nf b/src/nf_modules/bedtools/main.nf
index 70314d7c83f08070dd8fde307d4195e8a4acd1ae..ebf6893723f2c9c842ebb591334d3e7afb0d5662 100644
--- a/src/nf_modules/bedtools/main.nf
+++ b/src/nf_modules/bedtools/main.nf
@@ -28,11 +28,10 @@ process bam_to_fastq_singleend {
   publishDir "results/fasta/", mode: 'copy'
 
   input:
-  path fasta
-  path bed
+  path bam
 
   output:
-  path "*_extracted.fasta", emit: fasta
+  path "*.fastq", emit: fastq
 
   script:
 """
@@ -48,11 +47,10 @@ process bam_to_fastq_paired_end {
   publishDir "results/fasta/", mode: 'copy'
 
   input:
-  path fasta
-  path bed
+  path bam
 
   output:
-  path "*_extracted.fasta", emit: fasta
+  path "*.fastq", emit: fasta
 
   script:
 """
diff --git a/src/nf_modules/samtools/main.nf b/src/nf_modules/samtools/main.nf
index cf0d2158e7f62f9e71849639f5148456789311f3..83a5a177630acb370d67b7b0e649e8499d518d96 100644
--- a/src/nf_modules/samtools/main.nf
+++ b/src/nf_modules/samtools/main.nf
@@ -25,7 +25,6 @@ process filter_bam_mapped {
 
   input:
     tuple val(file_id), path(bam)
-    path bed
 
   output:
     tuple val(file_id), path("*_filtered.bam"), emit: bam
@@ -42,7 +41,6 @@ process filter_bam_unmapped {
 
   input:
     tuple val(file_id), path(bam)
-    path bed
 
   output:
     tuple val(file_id), path("*_filtered.bam"), emit: bam