diff --git a/subworkflows/local/kallisto_bustools.nf b/subworkflows/local/kallisto_bustools.nf
index d6b171a6..5f8d9bcc 100644
--- a/subworkflows/local/kallisto_bustools.nf
+++ b/subworkflows/local/kallisto_bustools.nf
@@ -66,7 +66,9 @@ workflow KALLISTO_BUSTOOLS {
 
     emit:
     ch_versions
-    counts          = ch_raw_counts.mix (ch_filtered_counts)
+    counts          = KALLISTOBUSTOOLS_COUNT.out.count
+    counts_raw      = ch_raw_counts
+    counts_filtered = ch_filtered_counts
     txp2gene        = txp2gene.collect()
 
 }
diff --git a/workflows/scrnaseq.nf b/workflows/scrnaseq.nf
index f7bbe692..070565f4 100644
--- a/workflows/scrnaseq.nf
+++ b/workflows/scrnaseq.nf
@@ -135,7 +135,7 @@ workflow SCRNASEQ {
             ch_fastq
         )
         ch_versions = ch_versions.mix(KALLISTO_BUSTOOLS.out.ch_versions)
-        ch_mtx_matrices = KALLISTO_BUSTOOLS.out.counts
+        ch_mtx_matrices = KALLISTO_BUSTOOLS.out.counts_raw.mix( KALLISTO_BUSTOOLS.out.counts_filtered )
         ch_txp2gene = KALLISTO_BUSTOOLS.out.txp2gene
     }
 
@@ -170,9 +170,7 @@ workflow SCRNASEQ {
         )
         ch_versions = ch_versions.mix(STARSOLO.out.ch_versions)
         ch_multiqc_files = ch_multiqc_files.mix(STARSOLO.out.for_multiqc)
-        ch_mtx_matrices =
-            STARSOLO.out.raw_counts.map{ meta, files -> [meta + [input_type: 'raw'], files] }
-            .mix( STARSOLO.out.filtered_counts.map{ meta, files -> [meta + [input_type: 'filtered'], files] } )
+        ch_mtx_matrices = STARSOLO.out.raw_counts.mix( STARSOLO.out.filtered_counts )
     }
 
     // Run cellranger pipeline