diff --git a/subworkflows/local/shortread_adapterremoval.nf b/subworkflows/local/shortread_adapterremoval.nf
index 735d3b8..b573be9 100644
--- a/subworkflows/local/shortread_adapterremoval.nf
+++ b/subworkflows/local/shortread_adapterremoval.nf
@@ -67,7 +67,7 @@ workflow SHORTREAD_ADAPTERREMOVAL {
                 [meta_new, reads]
             }
             .groupTuple()
-            .map { meta, fastq -> [meta, fastq] }
+            .map { meta, fastq -> [meta, fastq.flatten()] }
 
 
         CAT_FASTQ(ch_concat_fastq)
diff --git a/subworkflows/local/shortread_fastp.nf b/subworkflows/local/shortread_fastp.nf
index 04057b1..4626691 100644
--- a/subworkflows/local/shortread_fastp.nf
+++ b/subworkflows/local/shortread_fastp.nf
@@ -29,7 +29,7 @@ workflow SHORTREAD_FASTP {
                                             meta, reads ->
                                                 def meta_new = meta.clone()
                                                 meta_new['single_end'] = true
-                                                [ meta_new, reads.flatten() ]
+                                                [ meta_new, [ reads ].flatten() ]
                                         }
 
         ch_fastp_reads_prepped = ch_fastp_reads_prepped_pe.mix( FASTP_SINGLE.out.reads )