diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
index eb21b9d..db46f2b 100644
--- a/subworkflows/local/input_check.nf
+++ b/subworkflows/local/input_check.nf
@@ -45,7 +45,6 @@ def create_fastq_channel(LinkedHashMap row) {
     meta.run_accession          = row.run_accession
     meta.instrument_platform    = row.instrument_platform
     meta.single_end             = row.single_end.toBoolean()
-    meta.is_fasta               = false
 
     // add path(s) of the fastq file(s) to the meta map
     def fastq_meta = []
@@ -76,7 +75,6 @@ def create_fasta_channel(LinkedHashMap row) {
     meta.run_accession          = row.run_accession
     meta.instrument_platform    = row.instrument_platform
     meta.single_end             = true
-    meta.is_fasta               = true
 
     def array = []
     if (!file(row.fasta).exists()) {
diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf
index 156259b..4e0a3a9 100644
--- a/subworkflows/local/profiling.nf
+++ b/subworkflows/local/profiling.nf
@@ -76,19 +76,19 @@ workflow PROFILING {
 
     ch_input_for_centrifuge =  ch_input_for_profiling.centrifuge
                             .filter{
-                                    if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] Centrifuge currently does not accept FASTA files as input. Skipping Centrifuge for sample " + it[0].id
-                                    !it[0].is_fasta
+                                 if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] Centrifuge currently does not accept FASTA files as input. Skipping Centrifuge for sample " + it[0].id
+                                 !it[0].is_fasta
+                            }
+                            .multiMap {
+                                it ->
+                                   reads: [ it[0] + it[2], it[1] ]
+                                   db: it[3]
                             }
-                                .multiMap {
-                                    it ->
-                                        reads: [ it[0] + it[2], it[1] ]
-                                        db: it[3]
-                                }
 
     ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3
                             .filter{
-                                    if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] MetaPhlAn3 does not accept FASTA files as input. Skipping MetaPhlAn3 for sample " + it[0].id
-                                    !it[0].is_fasta
+                                if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] Centrifuge currently does not accept FASTA files as input. Skipping Centrifuge for sample " + it[0].id
+                                !it[0].is_fasta
                             }
                             .multiMap {
                                 it ->
diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf
index 884ee46..3ae1351 100644
--- a/workflows/taxprofiler.nf
+++ b/workflows/taxprofiler.nf
@@ -176,10 +176,10 @@ workflow TAXPROFILER {
                 [ meta, [ reads ].flatten() ]
             }
             .mix( INPUT_CHECK.out.fasta )
+
     } else {
         ch_reads_runmerged = ch_shortreads_hostremoved
-            .mix( ch_longreads_preprocessed )
-            .mix( INPUT_CHECK.out.fasta )
+            .mix( ch_longreads_preprocessed, INPUT_CHECK.out.fasta )
     }
 
     /*