fix input and output for bedtools and samtools

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:
 """

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