diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
index db46f2b..eb21b9d 100644
--- a/subworkflows/local/input_check.nf
+++ b/subworkflows/local/input_check.nf
@@ -45,6 +45,7 @@ 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 = []
@@ -75,6 +76,7 @@ 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 18de739..f2f7eb7 100644
--- a/subworkflows/local/profiling.nf
+++ b/subworkflows/local/profiling.nf
@@ -75,6 +75,10 @@ workflow PROFILING {
                             }
 
     ch_input_for_centrifuge =  ch_input_for_profiling.centrifuge
+                            .filter{
+                                    if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] Centrifuge 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] ]
@@ -82,6 +86,10 @@ workflow PROFILING {
                                 }
 
     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
+                            }
                             .multiMap {
                                 it ->
                                     reads: [it[0] + it[2], it[1]]
diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf
index 9fe8cc8..e7ff78b 100644
--- a/workflows/taxprofiler.nf
+++ b/workflows/taxprofiler.nf
@@ -19,11 +19,11 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
 // Check mandatory parameters
 if (params.input    ) { ch_input     = file(params.input)     } else { exit 1, 'Input samplesheet not specified!' }
 if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
-if (params.shortread_clipmerge_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] warning: MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
-if (params.shortread_clipmerge_excludeunmerged && !params.shortread_clipmerge_mergepairs) exit 1, "[nf-core/taxprofiler] error: cannot include unmerged reads when merging not turned on. Please specify --shortread_clipmerge_mergepairs"
+if (params.shortread_clipmerge_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler]: MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
+if (params.shortread_clipmerge_excludeunmerged && !params.shortread_clipmerge_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging not turned on. Please specify --shortread_clipmerge_mergepairs"
 
-if (params.perform_shortread_hostremoval && !params.shortread_hostremoval_reference) { exit 1, "[nf-core/taxprofiler] error: --shortread_hostremoval requested but no --shortread_hostremoval_reference FASTA supplied. Check input." }
-if (!params.shortread_hostremoval_reference && params.shortread_hostremoval_reference_index) { exit 1, "[nf-core/taxprofiler] error: --shortread_hostremoval_index provided but no --shortread_hostremoval_reference FASTA supplied. Check input." }
+if (params.perform_shortread_hostremoval && !params.shortread_hostremoval_reference) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval requested but no --shortread_hostremoval_reference FASTA supplied. Check input." }
+if (!params.shortread_hostremoval_reference && params.shortread_hostremoval_reference_index) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval_index provided but no --shortread_hostremoval_reference FASTA supplied. Check input." }
 
 if (params.shortread_hostremoval_reference ) { ch_reference       = file(params.shortread_hostremoval_reference) }
 if (params.shortread_hostremoval_index     ) { ch_reference_index = file(params.shortread_hostremoval_index    ) } else { ch_reference_index = [] }
@@ -175,10 +175,11 @@ workflow TAXPROFILER {
                 meta, reads ->
                 [ meta, [ reads ].flatten() ]
             }
-
+            .mix( INPUT_CHECK.out.fasta )
     } else {
         ch_reads_runmerged = ch_shortreads_hostremoved
             .mix( ch_longreads_preprocessed )
+            .mix( INPUT_CHECK.out.fasta )
     }
 
     /*