diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf
index 61eda6e..2d0c17d 100644
--- a/workflows/taxprofiler.nf
+++ b/workflows/taxprofiler.nf
@@ -140,8 +140,7 @@ workflow TAXPROFILER {
             }
             .groupTuple()
 
-        ch_reads_runmerged = CAT_FASTQ ( ch_reads_for_cat )
-
+        ch_reads_runmerged = CAT_FASTQ ( ch_reads_for_cat ).reads
     } else {
         ch_reads_runmerged = ch_shortreads_filtered
             .mix( ch_longreads_preprocessed )
@@ -247,6 +246,10 @@ workflow TAXPROFILER {
         ch_versions = ch_versions.mix( SHORTREAD_COMPLEXITYFILTERING.out.versions )
     }
 
+    if (params.run_merging){
+        ch_versions = ch_versions.mix(CAT_FASTQ.out.versions)
+    }
+
     if (params.run_kraken2) {
         ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([])  )
         ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() )