diff --git a/modules/lima/main.nf b/modules/lima/main.nf
index a662a7bb..691e43f2 100644
--- a/modules/lima/main.nf
+++ b/modules/lima/main.nf
@@ -12,9 +12,7 @@ process LIMA {
     path primers
 
     output:
-    tuple val(meta), path("*.clips")  , emit: clips
     tuple val(meta), path("*.counts") , emit: counts
-    tuple val(meta), path("*.guess")  , emit: guess
     tuple val(meta), path("*.report") , emit: report
     tuple val(meta), path("*.summary"), emit: summary
     path "versions.yml"               , emit: versions
@@ -27,10 +25,18 @@ process LIMA {
     tuple val(meta), path("*.fastq.gz")         , optional: true, emit: fastqgz
     tuple val(meta), path("*.xml")              , optional: true, emit: xml
     tuple val(meta), path("*.json")             , optional: true, emit: json
+    tuple val(meta), path("*.clips")            , optional: true, emit: clips
+    tuple val(meta), path("*.guess")            , optional: true, emit: guess
 
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    if( "$ccs" == "${prefix}.bam" )      error "Input and output names are the same, set prefix in module configuration"
+    if( "$ccs" == "${prefix}.fasta" )    error "Input and output names are the same, set prefix in module configuration"
+    if( "$ccs" == "${prefix}.fasta.gz" ) error "Input and output names are the same, set prefix in module configuration"
+    if( "$ccs" == "${prefix}.fastq" )    error "Input and output names are the same, set prefix in module configuration"
+    if( "$ccs" == "${prefix}.fastq.gz" ) error "Input and output names are the same, set prefix in module configuration"
+
     """
     OUT_EXT=""
 
@@ -46,7 +52,6 @@ process LIMA {
         OUT_EXT="fastq.gz"
     fi
 
-    echo \$OUT_EXT
     lima \\
         $ccs \\
         $primers \\