diff --git a/main.nf b/main.nf
index e883b9e..3727e82 100644
--- a/main.nf
+++ b/main.nf
@@ -29,11 +29,9 @@ if (!params.debug) {
 }
 
 // Adding the option to skip the alignment if skipAlignment is set to true.
-(fastqPairs_ch, bamPairs_ch) = ( params.skipAlignment
-                 ? [Channel.empty(), Channel.fromFilePairs( params.inputDir+'/'+params.inputPattern, checkIfExists: true )  ]
-                 : [Channel.fromFilePairs( params.inputDir+'/'+params.inputPattern, size: 2, checkIfExists: true ), Channel.empty() ] )
-
-bamPairs_ch.flatten().collate(3).set { newBamPairs_ch }
+(fastqPairs_ch, bamPairs_ch) = (params.skipAlignment
+                 ? [Channel.empty(), Channel.fromFilePairs(params.inputDir+'/'+params.inputPattern, size: 2, checkIfExists: true)  ]
+                 : [Channel.fromFilePairs(params.inputDir+'/'+params.inputPattern, size: 2, checkIfExists: true), Channel.empty() ] )
 
 process ERValign {
     tag "${sample}"
@@ -51,15 +49,13 @@ process ERValign {
     errorStrategy 'terminate'
 
     input:
-    tuple val(sample), path (reads) from fastqPairs_ch
+    tuple val (sample), path (reads) from fastqPairs_ch
     val (localOutputDir) from params.localOutputDir
     val (limitMemory) from params.limitMemory
     val (debug) from params.debug
     
     output:
     tuple sample, path ("${localOutputDir}/${sample}.Aligned.sortedByCoord.out.bam*") into star_bam_ch  
-    // path ("${localOutputDir}/${sample}.Aligned.sortedByCoord.out.bam.bai") into star_bai_ch
-    // val (sample) into prefix_ch
 
     when:
     !params.skipAlignment
@@ -67,34 +63,31 @@ process ERValign {
     shell:
     template 'ERValign.sh'
 }
-star_bam_ch.subscribe{ println "File: ${it.name} => ${it.text}" }
 
-// process ERVcount {
-//     tag "${sample}"
+process ERVcount {
+    tag "${sample}"
 
-//     // executor configuration
-//     time '3h'
-//     memory '8.GB'
-//     scratch true
-//     storeDir params.outputDir
+    // executor configuration
+    time '3h'
+    memory '8.GB'
+    scratch true
+    storeDir params.outputDir
 
-//     // other configuration
-//     echo true
-//     errorStrategy 'terminate'
-//     stageInMode 'symlink'
+    // other configuration
+    echo true
+    errorStrategy 'terminate'
+    stageInMode 'symlink'
     
-//     input:
-//     tuple val(sample), path (bam), path (bai) from newBamPairs_ch
-//     val (debug) from params.debug
-//     // path (bam) from bam_ch.mix(star_bam_ch) // mixing with the channel from ERValign if started from FASTQs and skipAlignment=false
-//     // path (bai) from bai_ch.mix(star_bai_ch)  // mixing with the channel from ERValign if started from FASTQs and skipAlignment=false
+    input:
+    tuple val (sample), path (bam) from bamPairs_ch.mix(star_bam_ch) // mixing with the channel from ERValign if started from FASTQs and skipAlignment=false
+    val (debug) from params.debug
     
-//     output: 
-//     path ("${sample}"+'.ERVresults.txt') into final_results_ch
+    output: 
+    path ("${sample}"+'.ERVresults.txt') into final_results_ch
 
-//     shell:
-//     template 'ERVcount.sh'
-// }
+    shell:
+    template 'ERVcount.sh'
+}
 
 // ~~~~~~~~~~~~~~~ PIPELINE COMPLETION EVENTS ~~~~~~~~~~~~~~~~~~~ //
 
diff --git a/templates/ERVcount.sh b/templates/ERVcount.sh
index 38a33b8..098d385 100644
--- a/templates/ERVcount.sh
+++ b/templates/ERVcount.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-BAM="!{bam}"
+BAM="!{bam[0]}"
 _DEBUG="!{debug}"
 
 logMsg() {