diff --git a/nextflow.config b/nextflow.config
index 6c39ccd..a8240d1 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -192,7 +192,7 @@ profiles {
     test      { includeConfig 'conf/test.config'      }
     test_full { includeConfig 'conf/test_full.config' }
     test_noprofiling { includeConfig 'conf/test_noprofiling.config' }
-    test_nopreprocessing { includeConfig 'conf/test_preprocessing.config' }
+    test_nopreprocessing { includeConfig 'conf/test_nopreprocessing.config' }
 }
 
 // Load igenomes.config if required
diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf
index 109598d..2813bc7 100644
--- a/subworkflows/local/profiling.nf
+++ b/subworkflows/local/profiling.nf
@@ -190,6 +190,10 @@ workflow PROFILING {
     if ( params.run_motus ) {
 
         ch_input_for_motus = ch_input_for_profiling.motus
+                                .filter{
+                                    if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] mOTUs currently does not accept FASTA files as input. Skipping mOTUs for sample ${it[0].id}."
+                                    !it[0].is_fasta
+                                }
                                 .multiMap {
                                     it ->
                                         reads: [it[0] + it[2], it[1]]