diff --git a/config/params.new.yml b/config/params.new.yml
new file mode 100644
index 0000000..511de15
--- /dev/null
+++ b/config/params.new.yml
@@ -0,0 +1,82 @@
+input:
+  local_dir: null
+  remote_dir: null
+  ignore_dirs: null
+  pacbio_reads: false
+  bam_input_pattern: null
+  large_reference: null
+  remove_file_suffix: null
+  custom_fastq_file_suffixes: null
+  do_bam2fq_conversion: false
+
+comms:
+  notify: null
+  mailer: "/usr/bin/mail"  
+
+output:
+  directory: "output"
+
+profilers:
+  gffquant:
+    run: true
+    stream: true
+    db: null
+    aligner: "bwa"
+    mode: "gene"
+    ambig_mode: "1overN"
+    strand_specific: null
+    single_end_library: false
+    do_name_sort: null
+    min_seqlen: 45
+    min_identity: 0.97
+    restrict_metrics: ""
+    keep_alignments: false
+    reference_index: null
+    collate_columns: "uniq_scaled,combined_scaled"
+    collate_gene_counts: true
+  metaphlan3:
+    run: false
+    db: null
+    db_version: null
+    params: null
+  metaphlan4:
+    run: false
+    db: null
+    samestr_compatible_output: false
+  samestr:
+    run: false
+    marker_db: null
+  motus:
+    run: false
+    db: null
+    tax_level: "mOTU"
+    min_length: 75
+    n_marker_genes: 3
+
+decon:
+  run: false
+  keep_chimeras: false
+  kraken2:
+    min_hit_groups: 10
+    db: "/scratch/schudoma/databases/kraken2/hg38_silva_genome"
+    fix_read_ids: false
+
+align:
+  run: false
+  reference_index: null
+
+qc:
+  run: true
+  keep_orphans: true
+  generate_reports: true
+  amplicon:
+    run: false
+    primers: null
+    minlen: 45
+    p5_primer_params: "cu=t qtrim=rl ktrim=l trimq=3 k=9 mink=1 hdist=1 restrictleft=50"
+    p3_primer_params: "cu=t ktrim=r k=9 mink=1 hdist=1 restrictright=50"
+    long_reads: false
+    single_end: false
+  shotgun:
+    params: "qtrim=rl trimq=3 maq=25 ktrim=r k=23 mink=11 hdist=1 ftm=5 entropy=0.5 entropywindow=50 entropyk=5 tpe tbo"
+    minlen: 45
diff --git a/main.nf b/main.nf
index 56d7b1a..0564eae 100644
--- a/main.nf
+++ b/main.nf
@@ -6,63 +6,33 @@ include { nevermore_main } from "./nevermore/workflows/nevermore"
 include { gffquant_flow } from "./nevermore/workflows/gffquant"
 include { fastq_input } from "./nevermore/workflows/input"
 
-if (params.input_dir && params.remote_input_dir) {
-	log.info """
-		Cannot process both --input_dir and --remote_input_dir. Please check input parameters.
-	""".stripIndent()
-	exit 1
-} else if (!params.input_dir && !params.remote_input_dir) {
-	log.info """
-		Neither --input_dir nor --remote_input_dir set.
-	""".stripIndent()
-	exit 1
-}
-
-def input_dir = (params.input_dir) ? params.input_dir : params.remote_input_dir
+include { get_single_input_dir } from "./nevermore/modules/functions/validation"
 
-params.ignore_dirs = ""
+def input_dir = get_single_input_dir()
 
+params.input.ignore_dirs = null
 
 
 workflow {
 
 	fastq_input(
 		Channel.fromPath(input_dir + "/*", type: "dir")
-			.filter { !params.ignore_dirs.split(",").contains(it.name) }
+			.filter { params.input.ignore_dirs and !params.input.ignore_dirs.split(",").contains(it.name) }
 	)
 
 	fastq_ch = fastq_input.out.fastqs
 	
 	nevermore_main(fastq_ch)
 
-	if (params.run_gffquant) {
-
-		if (params.gq_stream) {
-			gq_input_ch = nevermore_main.out.fastqs
-				.map { sample, fastqs ->
-				sample_id = sample.id.replaceAll(/.(orphans|singles|chimeras)$/, "")
-				return tuple(sample_id, [fastqs].flatten())
-			}
-			.groupTuple()
-			.map { sample_id, fastqs -> return tuple(sample_id, fastqs.flatten()) }
-			gq_input_ch.view()
-			//.groupTuple(sort: true)
-
-		} else {
-
-			gq_input_ch = nevermore_main.out.alignments
-
-		}
+	if (params.profilers.gffquant.run) {
 
-		// gq_input_ch = ((params.gq_stream) ? nevermore_main.out.fastqs : never_main.out.alignments)
-		// 	.map { sample, files -> return tuple(sample.id, files) }
-		gffquant_flow(gq_input_ch)		
+		gffquant_flow((params.profilers.gffquant.stream) ? nevermore_main.out.fastqs : nevermore_main.out.alignments)
 
 	}
 
-	if (params.run_motus) {
+	if (params.profilers.motus.run) {
 
-		motus(nevermore_main.out.fastqs, params.motus_db)
+		motus(nevermore_main.out.fastqs, params.profilers.motus.db)
 
 	}
 
diff --git a/nevermore/modules/collate.nf b/nevermore/modules/collate.nf
index 9dbf3ed..492aef6 100644
--- a/nevermore/modules/collate.nf
+++ b/nevermore/modules/collate.nf
@@ -1,5 +1,4 @@
 process collate_stats {
-    // publishDir params.output_dir, mode: params.publish_mode
 
     input:
     path(stats_files)
diff --git a/nevermore/modules/converters/bam2fq.nf b/nevermore/modules/converters/bam2fq.nf
index 3b449b1..38d433f 100644
--- a/nevermore/modules/converters/bam2fq.nf
+++ b/nevermore/modules/converters/bam2fq.nf
@@ -1,6 +1,5 @@
 process bam2fq {
-    // publishDir params.output_dir, mode: params.publish_mode
-
+    
     input:
     tuple val(sample), path(bam)
 
diff --git a/nevermore/modules/converters/fq2bam.nf b/nevermore/modules/converters/fq2bam.nf
index 3138e5d..a91e08b 100644
--- a/nevermore/modules/converters/fq2bam.nf
+++ b/nevermore/modules/converters/fq2bam.nf
@@ -1,3 +1,5 @@
+params.input.pacbio_reads = false
+
 process fq2bam {
     input:
     tuple val(sample), path(fq)
@@ -9,7 +11,7 @@ process fq2bam {
 	def maxmem = task.memory.toGiga()
 	def r2 = (sample.is_paired) ? "in2=${sample.id}_R2.fastq.gz" : ""
 	def qual_modifier = ""
-	if (params.pb_reads) {
+	if (params.input.pacbio_reads) {
 		qual_modifier = "qin=33"
 	}
 
diff --git a/nevermore/modules/converters/fq2fa.nf b/nevermore/modules/converters/fq2fa.nf
index 612e449..819981c 100644
--- a/nevermore/modules/converters/fq2fa.nf
+++ b/nevermore/modules/converters/fq2fa.nf
@@ -1,3 +1,5 @@
+params.input.pacbio_reads = false
+
 process fq2fa {
     input:
     tuple val(sample), path(fq)
@@ -9,7 +11,7 @@ process fq2fa {
 	def maxmem = task.memory.toGiga()
 	def r2 = (sample.is_paired) ? "in2=${sample.id}_R2.fastq.gz out2=out/${sample.id}_R2.fasta" : ""
 	def qual_modifier = ""
-	if (params.pb_reads) {
+	if (params.input.pacbio_reads) {
 		qual_modifier = "qin=33"
 	}
 
diff --git a/nevermore/modules/converters/prepare_fastqs.nf b/nevermore/modules/converters/prepare_fastqs.nf
index ba8043f..c7baecf 100644
--- a/nevermore/modules/converters/prepare_fastqs.nf
+++ b/nevermore/modules/converters/prepare_fastqs.nf
@@ -1,5 +1,4 @@
 process prepare_fastqs {
-    // publishDir params.output_dir, mode: params.publish_mode
 
     input:
     tuple val(sample), path(fq)
diff --git a/nevermore/modules/decon/dehumanise.nf b/nevermore/modules/decon/dehumanise.nf
deleted file mode 100644
index e279691..0000000
--- a/nevermore/modules/decon/dehumanise.nf
+++ /dev/null
@@ -1,57 +0,0 @@
-process dehumanise {
-    // publishDir "$output_dir", mode: params.publish_mode, pattern: "no_human/*/*.fastq.gz"
-
-    input:
-    tuple val(sample), path(fq)
-
-    output:
-    tuple val(sample), path("no_human/${sample}/${sample}.bam"), emit: bam
-    tuple val(sample), path("no_human/${sample}/${sample}*.fastq.gz"), emit: fq
-    tuple val("${sample}.full"), path("${sample}.full.bam"), emit: full_bam
-
-    script:
-    def in_fq = (fq.size() == 2) ? "in=${fq[0]} in2=${fq[1]}" : "in=${fq[0]}";
-    def maxmem = task.memory.toGiga()
-    """
-    set -o pipefail
-    mkdir -p no_human/${sample}
-    ln -s ${params.decon_ref}
-    bbmap.sh -Xmx${maxmem}g t=$task.cpus ${in_fq} outu=unmapped.sam outm=mapped.sam idfilter=${params.decon_minid}
-    cp unmapped.sam full.sam
-    samtools view mapped.sam >> full.sam
-    samtools view -f 4 mapped.sam >> unmapped.sam
-    samtools view -f 8 mapped.sam >> unmapped.sam
-
-    samtools collate -@ $task.cpus -O unmapped.sam | samtools view -buh > unmapped.bam
-
-    if [[ "\$?" -eq 0 ]];
-    then
-        samtools fastq -@ task.cpus -0 ${sample}_other.fastq.gz -1 ${sample}_R1.fastq.gz -2 ${sample}_R2.fastq.gz unmapped.bam
-        if  [[ "\$?" -eq 0 ]];
-        then
-
-            if [[ -z "\$(gzip -dc ${sample}_R1.fastq.gz | head -n 1)" ]];
-            then
-                if [[ ! -z "\$(gzip -dc ${sample}_other.fastq.gz | head -n 1)" ]];
-                then
-                    mv -v ${sample}_other.fastq.gz no_human/${sample}/${sample}_R1.fastq.gz;
-                fi;
-            else
-                    mv -v ${sample}_R1.fastq.gz no_human/${sample}/;
-                    if [[ ! -z "\$(gzip -dc ${sample}_R2.fastq.gz | head -n 1)" ]];
-                    then
-                        mv -v ${sample}_R2.fastq.gz no_human/${sample}/;
-                    fi;
-            fi;
-
-            mv -v unmapped.bam no_human/${sample}/${sample}.bam
-            ls -l *.fastq.gz
-            ls -l no_human/${sample}/
-            rm -rf *.fastq.gz
-
-            samtools view -buh full.sam > ${sample}.full.bam
-        fi;
-    fi;
-
-    """
-}
diff --git a/nevermore/modules/decon/kraken2.nf b/nevermore/modules/decon/kraken2.nf
index 81a9345..7bfeb18 100644
--- a/nevermore/modules/decon/kraken2.nf
+++ b/nevermore/modules/decon/kraken2.nf
@@ -1,3 +1,6 @@
+params.decon.kraken2.min_hit_groups = 10
+
+
 process remove_host_kraken2 {
 	label 'kraken2'
 
@@ -12,7 +15,7 @@ process remove_host_kraken2 {
     def out_options = (sample.is_paired) ? "--paired --unclassified-out ${sample.id}#.fastq" : "--unclassified-out ${sample.id}_1.fastq"
     def move_r2 = (sample.is_paired) ? "gzip -c ${sample.id}_2.fastq > no_host/${sample.id}/${sample.id}_R2.fastq.gz" : ""
 
-	def kraken2_call = "kraken2 --threads $task.cpus --db ${kraken_db} --report-minimizer-data --gzip-compressed --minimum-hit-groups ${params.kraken2_min_hit_groups}"
+	def kraken2_call = "kraken2 --threads $task.cpus --db ${kraken_db} --report-minimizer-data --gzip-compressed --minimum-hit-groups ${params.decon.kraken2.min_hit_groups}"
 
     """
     mkdir -p no_host/${sample.id}
@@ -40,10 +43,10 @@ process remove_host_kraken2_individual {
 	tuple val(sample), path("no_host/${sample.id}/KRAKEN_FINISHED"), emit: sentinel
 
 	script:
-	def kraken2_call = "kraken2 --threads $task.cpus --db ${kraken_db} --report-minimizer-data --gzip-compressed --minimum-hit-groups ${params.kraken2_min_hit_groups}"
+	def kraken2_call = "kraken2 --threads $task.cpus --db ${kraken_db} --report-minimizer-data --gzip-compressed --minimum-hit-groups ${params.decon.kraken2.min_hit_groups}"
 
 	fix_read_id_str = ""
-	if (params.fix_read_ids) {
+	if (params.decon.fix_read_ids) {
 		fix_read_id_str += "seqtk rename ${sample.id}_1.fastq read | cut -f 1 -d ' ' > ${sample.id}_1.fastq.renamed && mv -v ${sample.id}_1.fastq.renamed ${sample.id}_1.fastq\n"
 		fix_read_id_str += "seqtk rename ${sample.id}_2.fastq read | cut -f 1 -d ' ' > ${sample.id}_2.fastq.renamed && mv -v ${sample.id}_2.fastq.renamed ${sample.id}_2.fastq\n"
 	}
diff --git a/nevermore/modules/profilers/gffquant.nf b/nevermore/modules/profilers/gffquant.nf
index 4ad084f..e0cf98c 100644
--- a/nevermore/modules/profilers/gffquant.nf
+++ b/nevermore/modules/profilers/gffquant.nf
@@ -1,4 +1,29 @@
-params.gq_aligner = "bwa_mem"
+params.profilers.gffquant.aligner = "bwa"
+params.profilers.gffquant.collate_columns = "uniq_scaled,combined_scaled"
+
+
+def compile_param_string(sample_id, cpus, bam_input) {
+	def param_str = "-m ${params.profilers.gffquant.mode} --ambig_mode ${params.profilers.gffquant.ambig_mode}"
+	param_str += (params.profilers.gffquant.strand_specific) ? " --strand_specific" : ""
+	param_str += (params.profilers.gffquant.min_seqlen) ? (" --min_seqlen " + params.profilers.gffquant.min_seqlen) : ""
+	param_str += (params.profilers.gffquant.min_identity) ? (" --min_identity " + params.profilers.gffquant.min_identity) : ""
+	param_str += (params.profilers.gffquant.restrict_metrics) ? " --restrict_metrics ${params.profilers.gffquant.restrict_metrics}" : ""
+	param_str += " -t ${cpus}"
+
+	if (params.profilers.gffquant.gq_mode == "domain") {
+		param_str += " --db_separator , --db_coordinates hmmer"
+	}
+
+	if (bam_input) {
+		param_str += (params.profilers.gffquant.unmarked_orphans) ? " --unmarked_orphans" : ""
+		param_str += (params.input.bam_input_pattern || !params.input.large_reference) ? (" --format bam") : " --format sam" // not sure if that still works with recent gffquant versions?
+	} else {
+		param_str += (params.profilers.gffquant.keep_alignments) ? " --keep_alignment_file ${sample_id}.sam" : ""
+	}
+
+	return param_str
+}
+
 
 process stream_gffquant {
 	label "gffquant"
@@ -15,22 +40,11 @@ process stream_gffquant {
 	script:
 			def gq_output = "-o profiles/${sample}/${sample}"
 
-			def gq_params = "-m ${params.gq_mode} --ambig_mode ${params.gq_ambig_mode}"
-			gq_params += (params.gq_strand_specific) ? " --strand_specific" : ""
-			gq_params += (params.gq_min_seqlen) ? (" --min_seqlen " + params.gq_min_seqlen) : ""
-			gq_params += (params.gq_min_identity) ? (" --min_identity " + params.gq_min_identity) : ""
-			gq_params += (params.gq_restrict_metrics) ? " --restrict_metrics ${params.gq_restrict_metrics}" : ""
-			gq_params += (params.gq_keep_alignments) ? " --keep_alignment_file ${sample}.sam" : ""
-			gq_params += " -t ${task.cpus}"
-
-			if (params.gq_mode == "domain") {
-				gq_params += " --db_separator , --db_coordinates hmmer"
-			}
+			def gq_params = compile_param_string(sample, task.cpus, false)
 
 			def input_files = ""
-			// we cannot auto-detect SE vs. PE-orphan!
-			if (params.gq_single_end_library) {
-				//input_files += "--singles \$(find . -maxdepth 1 -type l -name '*_R1.fastq.gz')"	
+			// we cannot auto-detect SE vs. PE-orphan! --> i think this can be read from the sample object TODO!
+			if (params.profilers.gffquant.single_end_library) {
 				input_files += "--fastq-singles ${fastqs}"
 			} else {
 				r1_files = fastqs.findAll( { it.name.endsWith("_R1.fastq.gz") && !it.name.matches("(.*)(singles|orphans|chimeras)(.*)") } )
@@ -46,13 +60,10 @@ process stream_gffquant {
 				if (orphans.size() != 0) {
 					input_files += " --fastq-orphans ${orphans.join(' ')}"
 				}
-
-				// input_files += "--fastq-r1 \$(find . -maxdepth 1 -type l -name '*_R1.fastq.gz' | grep -v singles)"
-				// input_files += " --fastq-r2 \$(find . -maxdepth 1 -type l -name '*_R2.fastq.gz')"
-				// input_files += " --fastq-orphans \$(find . -maxdepth 1 -type l -name '*singles*.fastq.gz')"
+				
 			}
 	
-			def gq_cmd = "gffquant ${gq_output} ${gq_params} --db GQ_DATABASE --reference \$(readlink ${reference}) --aligner ${params.gq_aligner} ${input_files}"
+			def gq_cmd = "gffquant ${gq_output} ${gq_params} --db GQ_DATABASE --reference \$(readlink ${reference}) --aligner ${params.profilers.gffquant.aligner} ${input_files}"
 
 			"""
 			set -e -o pipefail
@@ -67,9 +78,10 @@ process stream_gffquant {
 
 process run_gffquant {
 	label "gffquant"
+	tag "gffquant.${sample}"
 
 	input:
-	tuple val(sample), path(alignments) //, path(readcounts)
+	tuple val(sample), path(alignments)
 	path(gq_db)
 
 	output:
@@ -79,27 +91,16 @@ process run_gffquant {
 	script:
 	def gq_output = "-o profiles/${sample}/${sample}"
 
-	def gq_params = "-m ${params.gq_mode} --ambig_mode ${params.gq_ambig_mode}"
-	gq_params += (params.gq_strand_specific) ? " --strand_specific" : ""
-	gq_params += (params.gq_unmarked_orphans) ? " --unmarked_orphans" : ""
-	gq_params += (params.gq_min_seqlen) ? (" --min_seqlen " + params.gq_min_seqlen) : ""
-	gq_params += (params.gq_min_identity) ? (" --min_identity " + params.gq_min_identity) : ""
-	// gq_params += (params.bam_input_pattern) ? " --import_readcounts \$(grep -o '[0-9]\\+' ${readcounts})" : ""
-	gq_params += (params.gq_restrict_metrics) ? " --restrict_metrics ${params.gq_restrict_metrics}" : ""
-	gq_params += (params.bam_input_pattern || !params.large_reference) ? (" --format bam") : " --format sam"
+	def gq_params = compile_param_string(sample, task.cpus, true)
 
-	def gq_cmd = "gffquant ${gq_output} ${gq_params} gq_db.sqlite3"
+	def gq_cmd = "gffquant ${gq_output} ${gq_params} GQ_DATABASE"
 
 	def mk_aln_sam = ""
-	if (params.bam_input_pattern) {
+	if (params.input.bam_input_pattern && params.profilers.gffquant.do_name_sort) {
 
-		if (params.do_name_sort) {
-			gq_cmd = "samtools collate -@ ${task.cpus} -O ${alignments} tmp/collated_bam | ${gq_cmd} -"
-		} else {
-			gq_cmd = "${gq_cmd} ${alignments}"
-		}
+		gq_cmd = "samtools collate -@ ${task.cpus} -O ${alignments} tmp/collated_bam | ${gq_cmd} --bam -"
 
-	} else if (params.large_reference) {
+	} else if (params.input.large_reference) {
 
 		mk_aln_sam += "echo 'Making alignment stream...'\n"
 		if (alignments instanceof Collection && alignments.size() >= 2) {
@@ -108,11 +109,11 @@ process run_gffquant {
 		} else {
 			mk_aln_sam += "ln -s ${alignments[0]} tmp/alignments.sam"
 		}
-		gq_cmd = "cat tmp/alignments.sam | ${gq_cmd} -"
+		gq_cmd = "cat tmp/alignments.sam | ${gq_cmd} --sam -"
 
 	} else {
 
-		gq_cmd = "${gq_cmd} ${alignments}"
+		gq_cmd = "${gq_cmd} --bam ${alignments}"
 
 	}
 
@@ -120,14 +121,14 @@ process run_gffquant {
 	set -e -o pipefail
 	mkdir -p logs/ tmp/ profiles/
 	echo 'Copying database...'
-	cp -v ${gq_db} gq_db.sqlite3
+	cp -v ${gq_db} GQ_DATABASE
 	${mk_aln_sam}
 	${gq_cmd} &> logs/${sample}.log
-	rm -rfv gq_db.sqlite3* tmp/
+	rm -rfv GQ_DATABASE* tmp/
 	"""
 }
 
-params.gq_collate_columns = "uniq_scaled,combined_scaled"
+
 
 process collate_feature_counts {
 
diff --git a/nevermore/modules/profilers/metaphlan3.nf b/nevermore/modules/profilers/metaphlan3.nf
index 351a843..a37d012 100644
--- a/nevermore/modules/profilers/metaphlan3.nf
+++ b/nevermore/modules/profilers/metaphlan3.nf
@@ -6,25 +6,22 @@ process run_metaphlan3 {
 
 	output:
 	tuple val(sample), path("metaphlan3_tables/${sample.id}.mp3.txt"), emit: mp3_table
-	// tuple val(sample), path("${sample.id}.bowtie2.bz2"), emit: mp3_bt2
 	
 	script:
-	def mp3_params = "--index ${params.mp3_db_version} --bowtie2db \$(readlink ${mp3_db}) --input_type fastq --nproc ${task.cpus} --tmp_dir tmp/"
+	def mp3_params = "--index ${params.profilers.metaphlan3.db_version} --bowtie2db \$(readlink ${params.profilers.metaphlan3.db}) --input_type fastq --nproc ${task.cpus} --tmp_dir tmp/"
 	def mp3_input = ""
 	def bt2_out = "--bowtie2out ${sample.id}.bowtie2.bz2"
 
 	
 	if (fastqs instanceof Collection && fastqs.size() >= 2) {
 		mp3_input = "${sample.id}_R1.fastq.gz,${sample.id}_R2.fastq.gz"
-	// } else if (fastqs instanceof Collection && fastqs.size() == 3) {
-	// 	mp3_input = "${sample.id}_R1.fastq.gz,${sample.id}_R2.fastq.gz,${sample.id}.singles_R1.fastq.gz"
 	} else {
 		mp3_input = "${fastqs}"
 	}
 
 	def additional_mp3_params = ""
-	if (params.mp3_params) {
-		additional_mp3_params = params.mp3_params
+	if (params.profilers.metaphlan3.params) {
+		additional_mp3_params = params.profilers.metaphlan3.params
 	}
 
 
diff --git a/nevermore/modules/profilers/metaphlan4.nf b/nevermore/modules/profilers/metaphlan4.nf
index 08946d8..60e2747 100644
--- a/nevermore/modules/profilers/metaphlan4.nf
+++ b/nevermore/modules/profilers/metaphlan4.nf
@@ -7,15 +7,14 @@ process run_metaphlan4 {
 	output:
 	tuple val(sample), path("${sample.id}.mp4.txt"), emit: mp4_table
 	tuple val(sample), path("${sample.id}.mp4.sam.bz2"), emit: mp4_sam, optional: (params.run_samestr || params.samestr_compatible_output)
-	// tuple val(sample), path("${sample.id}.bowtie2.bz2"), emit: mp4_bt2
 	
 	script:
 	def mp4_params = "--bowtie2db ${mp4_db} --input_type fastq --nproc ${task.cpus} --tmp_dir tmp/"
 	def mp4_input = ""
-	def bt2_out = "" //"--bowtie2out ${sample.id}.bowtie2.bz2"
+	def bt2_out = ""
 
 	def samestr_params = ""
-	if (params.run_samestr || params.samestr_compatible_output) {
+	if (params.profilers.samestr.run || params.profilers.metaphlan4.samestr_compatible_output) {
 		samestr_params = "--legacy-output -t rel_ab --samout ${sample.id}.mp4.sam.bz2"
 	}
 	
diff --git a/nevermore/modules/profilers/motus.nf b/nevermore/modules/profilers/motus.nf
index a12cb80..c3afb10 100644
--- a/nevermore/modules/profilers/motus.nf
+++ b/nevermore/modules/profilers/motus.nf
@@ -1,11 +1,9 @@
-params.motus_tax_level = "mOTU"
-params.motus_min_length = 75
-params.motus_n_marker_genes = 3
+params.profilers.motus.tax_level = "mOTU"
+params.profilers.motus.min_length = 75
+params.profilers.motus.n_marker_genes = 3
 
 
-process motus {
-    publishDir params.output_dir, mode: params.publish_mode
-
+process motus {    
     input:
     tuple val(sample), path(reads)
 	path(motus_db)
@@ -17,6 +15,6 @@ process motus {
     def motus_input = (sample.is_paired) ? "-f ${sample.id}_R1.fastq.gz -r ${sample.id}_R2.fastq.gz" : "-s ${sample.id}_R1.fastq.gz";
     """
     mkdir -p ${sample.id}
-    motus profile -t $task.cpus -k ${params.motus_tax_level} -c -v 7 -q -l ${params.motus_min_length} -g ${params.motus_n_marker_genes} -db ${motus_db} ${motus_input} > ${sample.id}/${sample.id}.motus.txt
+    motus profile -t $task.cpus -k ${params.profilers.motus.tax_level} -c -v 7 -q -l ${params.profilers.motus.min_length} -g ${params.profilers.motus.n_marker_genes} -db ${motus_db} ${motus_input} > ${sample.id}/${sample.id}.motus.txt
     """
 }
diff --git a/nevermore/modules/qc/bbduk.nf b/nevermore/modules/qc/bbduk.nf
index 9809e1f..0b51577 100644
--- a/nevermore/modules/qc/bbduk.nf
+++ b/nevermore/modules/qc/bbduk.nf
@@ -19,9 +19,9 @@ process qc_bbduk {
     def read2 = ""
     def orphan_check = ""
 
-    def bb_params = params.qc_params_shotgun //.replaceAll(/maq=([0-9]+)/, "")
+    def bb_params = params.qc.shotgun.params //.replaceAll(/maq=([0-9]+)/, "")
     
-    def trim_params = "${bb_params} ref=${adapters} minlen=${params.qc_minlen}"
+    def trim_params = "${bb_params} ref=${adapters} minlen=${params.qc.shotgun.minlen}"
 
     def orphan_filter = ""
     
diff --git a/nevermore/modules/qc/bbduk_amplicon.nf b/nevermore/modules/qc/bbduk_amplicon.nf
index df7ef89..1fd108c 100644
--- a/nevermore/modules/qc/bbduk_amplicon.nf
+++ b/nevermore/modules/qc/bbduk_amplicon.nf
@@ -15,18 +15,18 @@ process qc_bbduk_stepwise_amplicon {
 	def maxmem = task.memory.toGiga()
 	def compression = (reads[0].name.endsWith(".gz")) ? "gz" : "bz2"
 
-	if (params.primers) {
-		trim_params = "literal=${params.primers} minlength=${params.qc_minlen}"
+	if (params.qc.amplicon.primers) {
+		trim_params = "literal=${params.qc.amplicon.primers} minlength=${params.qc.amplicon.minlen}"
 	} else {
-		trim_params = "ref=${adapters} minlength=${params.qc_minlen}"
+		trim_params = "ref=${adapters} minlength=${params.qc.amplicon.minlen}"
 	}
 
 	def bbduk_call = "bbduk.sh -Xmx${maxmem}g t=${task.cpus} ordered=t trd=t"
 
-	ref_p5_r1 = (params.primers) ? "literal=" + params.primers.split(",")[0] : "ref=${adapters}"
-	ref_p5_r2 = (params.primers && !sample.is_paired) ? "literal=" + params.primers.split(",")[1] : "ref=${adapters}"
-	ref_p3_r1 = ref_p5_r2
-	ref_p3_r2 = ref_p5_r1
+	def ref_p5_r1 = (params.qc.amplicon.primers) ? "literal=" + params.qc.amplicon.primers.split(",")[0] : "ref=${adapters}"
+	def ref_p5_r2 = (params.qc.amplicon.primers && !sample.is_paired) ? "literal=" + params.qc.amplicon.primers.split(",")[1] : "ref=${adapters}"
+	def ref_p3_r1 = ref_p5_r2
+	def ref_p3_r2 = ref_p5_r1
 
 	def bbduk_full_call = ""
 	def downstream_call = ""
@@ -34,13 +34,13 @@ process qc_bbduk_stepwise_amplicon {
 
 	if (sample.is_paired) {
 
-		bbduk_full_call += "${bbduk_call} ${ref_p5_r1} minlength=${params.qc_minlen} ${params.p5_primer_params} in1=${sample.id}_R1.fastq.${compression} out1=fwd_p5.fastq.gz\n"
-		bbduk_full_call += "${bbduk_call} ${ref_p5_r2} minlength=${params.qc_minlen} ${params.p5_primer_params} in1=${sample.id}_R2.fastq.${compression} out1=rev_p5.fastq.gz\n"
+		bbduk_full_call += "${bbduk_call} ${ref_p5_r1} minlength=${params.qc.amplicon.minlen} ${params.qc.amplicon.p5_primer_params} in1=${sample.id}_R1.fastq.${compression} out1=fwd_p5.fastq.gz\n"
+		bbduk_full_call += "${bbduk_call} ${ref_p5_r2} minlength=${params.qc.amplicon.minlen} ${params.qc.amplicon.p5_primer_params} in1=${sample.id}_R2.fastq.${compression} out1=rev_p5.fastq.gz\n"
 
-		if (params.long_reads) {
+		if (params.qc.amplicon.long_reads) {
 
-			bbduk_full_call += "${bbduk_call} ${ref_p3_r1} minlength=${params.qc_minlen} ${params.p3_primer_params} in1=fwd_p5.fastq.gz out1=fwd.fastq.gz\n"
-			bbduk_full_call += "${bbduk_call} ${ref_p3_r2} minlength=${params.qc_minlen} ${params.p3_primer_params} in1=rev_p5.fastq.gz out1=rev.fastq.gz\n"
+			bbduk_full_call += "${bbduk_call} ${ref_p3_r1} minlength=${params.qc.amplicon.minlen} ${params.qc.amplicon.p3_primer_params} in1=fwd_p5.fastq.gz out1=fwd.fastq.gz\n"
+			bbduk_full_call += "${bbduk_call} ${ref_p3_r2} minlength=${params.qc.amplicon.minlen} ${params.qc.amplicon.p3_primer_params} in1=rev_p5.fastq.gz out1=rev.fastq.gz\n"
 
 		} else {
 			bbduk_full_call += "mv fwd_p5.fastq.gz fwd.fastq.gz\nmv rev_p5.fastq.gz rev.fastq.gz\n"
diff --git a/nevermore/modules/qc/multiqc.nf b/nevermore/modules/qc/multiqc.nf
index 472e905..4909ba2 100644
--- a/nevermore/modules/qc/multiqc.nf
+++ b/nevermore/modules/qc/multiqc.nf
@@ -1,6 +1,5 @@
 process multiqc {
-    // publishDir params.output_dir, mode: params.publish_mode
-
+    
     input:
     path(reports)
 	path(multiqc_config)
@@ -10,7 +9,7 @@ process multiqc {
     path("reports/${stage}.multiqc_report.html")
 
     script:
-    def send_report = (false && params.email && params.mailer) ? "echo . | ${params.mailer} -s 'multiqc_report' -a reports/${stage}.multiqc_report.html ${params.email}" : ""
+    def send_report = (false && params.comms.email && params.comms.mailer) ? "echo . | ${params.comms.mailer} -s 'multiqc_report' -a reports/${stage}.multiqc_report.html ${params.comms.email}" : ""
     """
 	mkdir -p reports/
     multiqc -o reports/ -n ${stage}.multiqc_report.html -c ${multiqc_config} .
diff --git a/nevermore/modules/stats.nf b/nevermore/modules/stats.nf
index a493cff..6a301c3 100644
--- a/nevermore/modules/stats.nf
+++ b/nevermore/modules/stats.nf
@@ -1,6 +1,5 @@
 process flagstats {
-    // publishDir params.output_dir, mode: params.publish_mode
-
+    
     input:
     tuple val(sample), path(bam)
 
diff --git a/nevermore/modules/validation/functions.nf b/nevermore/modules/validation/functions.nf
new file mode 100644
index 0000000..82c2c70
--- /dev/null
+++ b/nevermore/modules/validation/functions.nf
@@ -0,0 +1,16 @@
+
+
+def get_single_input_dir {
+	if (params.input.local_dir && params.input.remote_dir) {
+		log.info """
+			Cannot process both --input.local_dir and --input.remote_dir. Please check input parameters.
+		""".stripIndent()
+		exit 1
+	} else if (!params.input.local_dir && !params.input.remote_dir) {
+		log.info """
+			Please set either --input.local_dir or --input.remote_dir.
+		""".stripIndent()
+		exit 1
+	}
+	return (params.input.local_dir) ? params.input.local_dir : params.input.remote_dir
+}
diff --git a/nevermore/workflows/align.nf b/nevermore/workflows/align.nf
index e03055a..6185401 100644
--- a/nevermore/workflows/align.nf
+++ b/nevermore/workflows/align.nf
@@ -57,7 +57,10 @@ workflow nevermore_prep_align {
 			}
 		.set { single_reads_ch }
 
-		def se_group_size = 3 - (params.drop_chimeras ? 1 : 0) - (params.drop_orphans ? 1 : 0)
+		def expect_orphans = params.qc.run && params.qc.keep_orphans
+		def expect_chimeras = params.qc.run && params.decon.run && params.decon.keep_chimeras
+
+		def se_group_size = 3 - (expect_orphans ? 0 : 1) - (expect_chimeras ? 0 : 1)
 
 		single_reads_ch.paired_end
 			.groupTuple(sort: true, size: se_group_size, remainder: true)
@@ -68,68 +71,6 @@ workflow nevermore_prep_align {
 			.set { pe_singles_ch }
 
 		merged_single_ch = pe_singles_ch.merge
-		
-
-
-			// .map { sample, fastq  ->
-			// 	return tuple(sample.id, fastq)
-			// }
-			// .map { sample_id, files ->
-			// 	def meta = [:]
-			// 	meta.id = sample_id
-			// 	meta.is_paired = false
-			// 	meta.library = "paired"
-			// 	meta.merged = true
-			// 	return tuple(meta, files)
-			// }
-
-		// merged_single_ch = single_reads_ch.single_end
-		// 	.map { sample, fastq  ->
-		// 		return tuple(sample.id, fastq)
-		// 	}
-		// 	.groupTuple(sort: true)
-		// 	.map { sample_id, files ->
-		// 		def meta = [:]
-		// 		meta.id = sample_id
-		// 		meta.is_paired = false
-		// 		meta.library = "single"
-		// 		meta.merged = true
-		// 		return tuple(meta, files)
-		// 	}
-		// 	.concat(
-		// 		single_reads_ch.paired_end
-		// 			.map { sample, fastq  ->
-		// 				return tuple(sample.id, fastq)
-		// 			}
-		// 			.groupTuple(sort: true)
-		// 			.map { sample_id, files ->
-		// 				def meta = [:]
-		// 				meta.id = sample_id
-		// 				meta.is_paired = false
-		// 				meta.library = "paired"
-		// 				meta.merged = true
-		// 				return tuple(meta, files)
-		// 			}
-		// 	)
-
-		// merged_single_ch.view()
-		// merged_single_ch = single_ch
-		// 	.map { sample, fastq ->
-		// 		return tuple(
-		// 			sample.id.replaceAll(/.(orphans|singles|chimeras)$/, ".singles"),
-		// 			sample.library,
-		// 			fastq
-		// 		)
-		// 	}
-		// 	.groupTuple(sort: true)
-		// 	.map { sample_id, library, files ->
-		// 		def meta = [:]
-		// 		meta.id = sample_id
-		// 		meta.is_paired = false
-		// 		meta.library = library
-		// 		meta.merged = true
-		// 		return tuple(meta, files)
-		// 	}
 
 		/*	then merge single-read file groups into single files */
 
@@ -193,7 +134,7 @@ workflow nevermore_align {
 
 		bwa_mem_align(
 			fastq_ch,
-			params.reference,
+			params.align.reference_index,
 			true
 		)
 
diff --git a/nevermore/workflows/gffquant.nf b/nevermore/workflows/gffquant.nf
index 24ade25..6b69e12 100644
--- a/nevermore/workflows/gffquant.nf
+++ b/nevermore/workflows/gffquant.nf
@@ -1,21 +1,7 @@
 include { stream_gffquant; run_gffquant; collate_feature_counts } from "../modules/profilers/gffquant"
 
-params.gq_collate_columns = "uniq_scaled,combined_scaled"
-
-
-// workflow gffquant_stream {
-// 	take:
-// 		fastq_ch
-// 	main:
-// 		gq_stream_ch = fastq_ch
-// 			.map {
-// 				sample, files -> return tuple(sample.id, files)
-// 			}
-// 		stream_gffquant(gq_stream_ch, params.gffquant_db)
-// 	emit:
-
-// }
-
+params.profilers.gffquant.collate_columns = "uniq_scaled,combined_scaled"
+params.profilers.gffquant.collate_gene_counts = true
 
 workflow gffquant_flow {
 
@@ -25,21 +11,32 @@ workflow gffquant_flow {
 
 	main:
 
-		if (params.gq_stream) {
-			stream_gffquant(input_ch, params.gffquant_db, params.reference)
+		if (params.profilers.gffquant.stream) {
+			gq_input_ch = input_ch
+				.map { sample, fastqs ->
+				sample_id = sample.id.replaceAll(/.(orphans|singles|chimeras)$/, "")
+				return tuple(sample_id, [fastqs].flatten())
+			}
+			.groupTuple()
+			.map { sample_id, fastqs -> return tuple(sample_id, fastqs.flatten()) }
+			
+			stream_gffquant(gq_input_ch, params.profilers.gffquant.db, params.profilers.gffquant.reference_index)
 			feature_count_ch = stream_gffquant.out.results
 			counts = stream_gffquant.out.results
+
 		} else {
-			run_gffquant(input_ch, params.gffquant_db)
+
+			run_gffquant(input_ch, params.profilers.gffquant.db)
 			feature_count_ch = run_gffquant.out.results
 			counts = run_gffquant.out.results
+
 		}
 
 		feature_count_ch = feature_count_ch
 			.map { sample, files -> return files }
 			.flatten()
 			.filter { !it.name.endsWith("Counter.txt.gz") }
-			.filter { params.collate_gene_counts || !it.name.endsWith("gene_counts.txt.gz") }
+			.filter { params.profilers.gffquant.collate_gene_counts || !it.name.endsWith("gene_counts.txt.gz") }
 			.map { file -> 
 				def category = file.name
 					.replaceAll(/\.txt\.gz$/, "")
@@ -48,14 +45,14 @@ workflow gffquant_flow {
 			}
 			.groupTuple(sort: true)
 			.combine(
-				Channel.from(params.gq_collate_columns.split(","))
+				Channel.from(params.profilers.gffquant.collate_columns.split(","))
 			)
 
 		collate_feature_counts(feature_count_ch)
 
 	emit:
 
-		counts // = run_gffquant.out.results
+		counts
 		collated = collate_feature_counts.out.collated
 
 }
diff --git a/nevermore/workflows/input.nf b/nevermore/workflows/input.nf
index 53a8051..3bbbb45 100644
--- a/nevermore/workflows/input.nf
+++ b/nevermore/workflows/input.nf
@@ -2,14 +2,9 @@ nextflow.enable.dsl=2
 
 include { classify_sample; classify_sample_with_library_info } from "../modules/functions"
 
+params.input.bam_input_pattern = "**.bam"
 
-if (!params.bam_input_pattern) {
-	params.bam_input_pattern = "**.bam"
-}
-
-def bam_suffix_pattern = params.bam_input_pattern.replaceAll(/\*/, "")
-
-def input_dir = (params.input_dir) ? params.input_dir : params.remote_input_dir
+def bam_suffix_pattern = params.input.bam_input_pattern.replaceAll(/\*/, "")
 
 
 process transfer_fastqs {
@@ -49,11 +44,10 @@ process prepare_fastqs {
 
   script:
 		def remote_option = (remote_input) ? "--remote-input" : ""
-		def remove_suffix = (params.suffix_pattern) ? "--remove-suffix ${params.suffix_pattern}" : ""
-		def input_dir_prefix = (params.input_dir) ? params.input_dir : params.remote_input_dir
-
-		def custom_suffixes = (params.custom_fastq_file_suffixes) ? "--valid-fastq-suffixes ${params.custom_fastq_file_suffixes}" : ""
+		def remove_suffix = (params.input.remove_file_suffix) ? "--remove-suffix ${params.input.remove_file_suffix}" : ""
+		def input_dir_prefix = (params.input.local_dir) ? params.input.local_dir : params.input.remote_dir
 
+		def custom_suffixes = (params.input.custom_fastq_file_suffixes) ? "--valid-fastq-suffixes ${params.input.custom_fastq_file_suffixes}" : ""
 		def libsfx_param = (library_suffix != null) ? "--add_sample_suffix ${library_suffix}" : ""
 		
 		"""
@@ -62,11 +56,6 @@ process prepare_fastqs {
 }
 
 
-
-
-
-
-
 workflow remote_fastq_input {
 	take:
 		fastq_ch
@@ -98,7 +87,7 @@ workflow fastq_input {
 		libsfx
 	
 	main:
-		prepare_fastqs(fastq_ch.collect(), (params.remote_input_dir != null || params.remote_input_dir), libsfx)
+		prepare_fastqs(fastq_ch.collect(), (params.input.remote_dir != null || params.input.remote_dir), libsfx)
 
 		library_info_ch = prepare_fastqs.out.library_info
 			.splitCsv(header:false, sep:'\t', strip:true)
@@ -137,7 +126,7 @@ workflow bam_input {
 		bam_ch
 	main:
 
-		if (params.remote_input_dir) {
+		if (params.input.remote_dir) {
 			bam_ch = remote_bam_input(bam_ch.collect())
 		}
 
@@ -149,7 +138,7 @@ workflow bam_input {
 			.groupTuple(sort: true)
 			.map { classify_sample(it[0], it[1]) }
 
-		if (params.do_bam2fq_conversion) {
+		if (params.input.do_bam2fq_conversion) {
 			bam2fq(bam_ch)
 			bam_ch = bam2fq.out.reads
 				.map { classify_sample(it[0].id, it[1]) }
diff --git a/nevermore/workflows/nevermore.nf b/nevermore/workflows/nevermore.nf
index c4cf8b2..a833546 100644
--- a/nevermore/workflows/nevermore.nf
+++ b/nevermore/workflows/nevermore.nf
@@ -11,9 +11,6 @@ include { multiqc } from "../modules/qc/multiqc"
 include { collate_stats } from "../modules/collate"
 include { nevermore_align; nevermore_prep_align } from "./align"
 
-def do_preprocessing = (!params.skip_preprocessing || params.run_preprocessing)
-def do_alignment = params.run_gffquant || !params.skip_alignment
-def do_stream = params.gq_stream
 
 workflow nevermore_main {
 
@@ -22,12 +19,12 @@ workflow nevermore_main {
 		
 
 	main:
-		if (do_preprocessing) {
+		if (params.qc.run) {
 	
 			nevermore_simple_preprocessing(fastq_ch)
 	
 			preprocessed_ch = nevermore_simple_preprocessing.out.main_reads_out
-			if (!params.drop_orphans) {
+			if (params.qc.keep_orphans) {
 				preprocessed_ch = preprocessed_ch.concat(nevermore_simple_preprocessing.out.orphan_reads_out)
 			}
 
@@ -46,12 +43,12 @@ workflow nevermore_main {
 
 			}
 	
-			if (params.remove_host) {
+			if (params.decon.run) {
 	
-				remove_host_kraken2_individual(preprocessed_ch, params.remove_host_kraken2_db)
+				remove_host_kraken2_individual(preprocessed_ch, params.decon.kraken2.db)
 	
 				preprocessed_ch = remove_host_kraken2_individual.out.reads
-				if (!params.drop_chimeras) {
+				if (params.decon.keep_chimeras) {
 					chimera_ch = remove_host_kraken2_individual.out.chimera_orphans
 						.map { sample, file ->
 							def meta = sample.clone()
@@ -74,7 +71,7 @@ workflow nevermore_main {
 		align_ch = Channel.empty()
 		collate_ch = Channel.empty()
 
-		if (do_preprocessing) {
+		if (params.qc.run) {
 			collate_ch = nevermore_simple_preprocessing.out.raw_counts
 			.map { sample, file -> return file }
 			.collect()
@@ -85,11 +82,11 @@ workflow nevermore_main {
 			)
 		}
 
-		if (!do_stream && do_alignment) {
+		if (params.align.run || (params.profilers.gffquant.run && !params.profilers.gffquant.stream)) {
 			nevermore_align(nevermore_prep_align.out.fastqs)
 			align_ch = nevermore_align.out.alignments
 	
-			if (do_preprocessing) {		
+			if (params.qc.run) {		
 				collate_ch = collate_ch	
 					.concat(
 						nevermore_align.out.aln_counts
@@ -99,7 +96,7 @@ workflow nevermore_main {
 			}
 		}
 
-		if (do_preprocessing && params.run_qa) {
+		if (params.qc.run && params.qc.generate_reports) {
 			collate_stats(collate_ch.collect())
 		}
 
diff --git a/nevermore/workflows/prep.nf b/nevermore/workflows/prep.nf
index f035b0a..b5118cb 100644
--- a/nevermore/workflows/prep.nf
+++ b/nevermore/workflows/prep.nf
@@ -8,8 +8,8 @@ include { qc_bbmerge } from "../modules/qc/bbmerge"
 include { fastqc } from "../modules/qc/fastqc"
 include { multiqc } from "../modules/qc/multiqc"
 
-def merge_pairs = (params.merge_pairs || false)
-def keep_orphans = (params.keep_orphans || false)
+params.qc.keep_orphans = true
+
 
 def asset_dir = "${projectDir}/nevermore/assets"
 
@@ -38,7 +38,7 @@ workflow nevermore_simple_preprocessing {
 
 	main:
 		rawcounts_ch = Channel.empty()
-		if (params.run_qa) {
+		if (params.qc.generate_reports) {
 			fastqc(fastq_ch, "raw")
 
 			multiqc(
@@ -52,7 +52,7 @@ workflow nevermore_simple_preprocessing {
 		processed_reads_ch = Channel.empty()
 		orphans_ch = Channel.empty()
 
-		if (params.amplicon_seq) {
+		if (params.qc.amplicon.run) {
 
 			qc_bbduk_stepwise_amplicon(fastq_ch, "${asset_dir}/adapters.fa")
 			processed_reads_ch = processed_reads_ch.concat(qc_bbduk_stepwise_amplicon.out.reads)
@@ -106,7 +106,7 @@ workflow nevermore_preprocessing {
 
 		/* merge_pairs implies that we want to keep the merged reads, which are 'longer single-ends' */
 
-		if (merge_pairs) {
+		if (params.qc.merge_pairs) {
 
 			/* attempt to merge the paired-end reads */
 
@@ -114,7 +114,7 @@ workflow nevermore_preprocessing {
 
 			/* join the orphans (potentially empty, s. a.) and the merged reads as all are single-end */
 
-			if (keep_orphans) {
+			if (params.qc.keep_orphans) {
 				single_reads_ch = orphan_reads_ch
 					.join(qc_bbmerge.out.merged, remainder: true)
 					.map { sample, orphans, merged ->
@@ -148,7 +148,7 @@ workflow nevermore_preprocessing {
 
 			single_out_ch = singlelib_reads_ch
 
-			if (keep_orphans) {
+			if (params.qc.keep_orphans) {
 
 				single_out_ch = single_out_ch
 					.concat(concat_singles.out.reads)
diff --git a/nevermore/workflows/samestr.nf b/nevermore/workflows/samestr.nf
index e3ba50a..6cdb1b4 100644
--- a/nevermore/workflows/samestr.nf
+++ b/nevermore/workflows/samestr.nf
@@ -1,6 +1,6 @@
 include { run_samestr_convert; run_samestr_merge; run_samestr_filter; run_samestr_stats; run_samestr_compare; run_samestr_summarize } from "../modules/profilers/samestr"
 
-params.samestr_marker_db = "/scratch/schudoma/databases/samestr/mpa_vOct22_CHOCOPhlAnSGB_202212/marker_db/"
+params.profilers.samestr.marker_db = "/scratch/schudoma/databases/samestr/mpa_vOct22_CHOCOPhlAnSGB_202212/marker_db/"
 
 workflow samestr {
     take:
@@ -9,7 +9,7 @@ workflow samestr {
     main:
         run_samestr_convert(
 			samestr_convert_ch,
-			params.samestr_marker_db
+			params.profilers.samestr.marker_db
 		)
 
         Channel
@@ -25,7 +25,7 @@ workflow samestr {
 		run_samestr_merge(grouped_npy_ch)
 		run_samestr_filter(
 			run_samestr_merge.out.sstr_npy
-			params.samestr_marker_db
+			params.profilers.samestr.marker_db
 		)
 		run_samestr_stats(run_samestr_filter.out.sstr_npy)
 		run_samestr_compare(run_samestr_filter.out.sstr_npy)
diff --git a/nextflow.config b/nextflow.config
index ddc9ff6..09e4f15 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -4,5 +4,5 @@ manifest {
 	description = "Metagenomic functional profiling pipeline"
 	name = "nevermore"
 	nextflowVersion = ">=21.10.4"
-	version = "0.8.1"
+	version = "1.0"
 }