Split the bed file into a seperate input

modules/vardictjava/main.nf

@@ -8,7 +8,8 @@ process VARDICTJAVA {
         'quay.io/biocontainers/vardict-java:1.8.3--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(bam), path(regions_of_interest)
+    tuple val(meta), path(bam) 
+    path(regions_of_interest)
     path(reference_fasta)
 
     output:
@@ -23,14 +24,11 @@ process VARDICTJAVA {
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    head -n 20 $reference_fasta
-    cat $reference_fasta | wc -l
-
     vardict-java \\
         $args \\
         -b $bam \\
         -th $task.cpus \\
-        -n $prefix \\
+        -N $prefix \\
         -G $reference_fasta \\
         $regions_of_interest \\
         > ${prefix}.vcf

tests/modules/vardictjava/main.nf

@@ -6,14 +6,14 @@ include { VARDICTJAVA } from '../../../modules/vardictjava/main.nf'
 
 workflow test_vardictjava {
     
-    input = [
+    bam_input_ch = Channel.of([
         [ id:'test', single_end:false ], // meta map
         file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-    ]
+    ])
 
-    VARDICTJAVA ( 
-        input, 
-        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) 
-    )
+    bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    VARDICTJAVA ( bam_input_ch, bed, fasta )
 }