diff --git a/subworkflows/local/generate_downstream_samplesheets/main.nf b/subworkflows/local/generate_downstream_samplesheets/main.nf
index 2be09249..bc2600a2 100644
--- a/subworkflows/local/generate_downstream_samplesheets/main.nf
+++ b/subworkflows/local/generate_downstream_samplesheets/main.nf
@@ -7,20 +7,30 @@ workflow GENERATE_DOWNSTREAM_SAMPLESHEETS {
     ch_reads
 
     main:
-    ch_header  = Channel.empty()
     format     = 'csv' // most common format in nf-core
     format_sep = ','
-
     // Make your samplesheet channel construct here depending on your downstream pipelines
-    if ( params.generate_pipeline_samplesheets == 'taxprofiler' ) {
+    if ( params.generate_pipeline_samplesheets == 'taxprofiler' && params.save_clipped_reads ) { // save_clipped_reads must be true
+        def fastq_rel_path = '/'
+        if (params.bbnorm) {
+            fastq_rel_path = '/bbmap/bbnorm/'
+        } else if (!params.keep_phix) {
+            fastq_rel_path = '/QC_shortreads/remove_phix/'
+        }
+        else if (params.host_fasta) {
+            fastq_rel_path = '/QC_shortreads/remove_host/'
+        }
+        else if (!params.skip_clipping) {
+            fastq_rel_path = '/QC_shortreads/fastp/'
+        }
         ch_list_for_samplesheet = ch_reads
             .map {
                 meta, fastq ->
                     def sample              = meta.id
                     def run_accession       = meta.id
                     def instrument_platform = ""
-                    def fastq_1             = file(params.outdir).toString() + '/' + fastq[0].getName()
-                    def fastq_2             = file(params.outdir).toString() + '/' + fastq[1].getName()
+                    def fastq_1             = file(params.outdir).toString() + fastq_rel_path + meta.id + '/' + fastq[0].getName()
+                    def fastq_2             = file(params.outdir).toString() + fastq_rel_path + meta.id + '/' + fastq[1].getName()
                     def fasta               = ""
                 [ sample: sample, run_accession: run_accession, instrument_platform: instrument_platform, fastq_1: fastq_1, fastq_2: fastq_2, fasta: fasta ]
             }
diff --git a/workflows/mag.nf b/workflows/mag.nf
index c06c9892..ff2e0dc6 100644
--- a/workflows/mag.nf
+++ b/workflows/mag.nf
@@ -1009,7 +1009,6 @@ workflow MAG {
     ch_input_for_samplesheet = Channel
                             .empty()
                             .mix( ch_short_reads_assembly )
-                            .view()
 
     if ( params.generate_downstream_samplesheets ) {
         GENERATE_DOWNSTREAM_SAMPLESHEETS ( ch_input_for_samplesheet )