diff --git a/main.nf b/main.nf
index 93beb95..34fd95f 100755
--- a/main.nf
+++ b/main.nf
@@ -13,6 +13,11 @@ include { VARIANT_ANNOTATION; VARIANT_SARSCOV2_ANNOTATION;
             VARIANT_VAF_ANNOTATION; VAFATOR } from './modules/06_variant_annotation'
 include { PANGOLIN_LINEAGE; VCF2FASTA } from './modules/07_lineage_annotation'
 include { BGZIP } from './modules/08_compress_vcf'
+include { FASTQC; NANOPLOT } from './modules/09_ont_qc'
+include { NANOFILT; PORECHOP; CHOPPER; PORECHOP_ABI; MINIMAP2 } from './modules/10_ont_preprocess'
+include { OPTIMUS_NO_PRIME; PRIMER_SOFTCLIP } from './modules/11_ont_primer_removal'
+include { NANOCALLER; CLAIR3 } from './modules/12_ont_variant_calling'
+
 
 
 params.help= false
@@ -60,6 +65,8 @@ params.input_fastqs_list = false
 params.input_fastas_list = false
 params.input_vcfs_list = false
 params.input_bams_list = false
+params.input_ont = false
+
 
 if (params.help) {
     log.info params.help_message
@@ -239,42 +246,55 @@ workflow {
             bam_files = ALIGNMENT_PAIRED_END.out
         }
         else {
-            READ_TRIMMING_SINGLE_END(input_fastqs)
-            ALIGNMENT_SINGLE_END(READ_TRIMMING_SINGLE_END.out[0], reference)
-            bam_files = ALIGNMENT_SINGLE_END.out
-        }
-        BAM_PREPROCESSING(bam_files, reference)
-        preprocessed_bams = BAM_PREPROCESSING.out.preprocessed_bams
-
-        if (primers) {
-            PRIMER_TRIMMING_IVAR(preprocessed_bams, primers)
-            preprocessed_bams = PRIMER_TRIMMING_IVAR.out.trimmed_bam
+	    if (params.input_ont) {
+	        FASTQC(input_fastqs)
+		PORECHOP(input_fastqs)
+		CHOPPER(PORECHOP.out.fq)
+		NANOPLOT(CHOPPER.out.fq)
+		input_bams = MINIMAP2(CHOPPER.out.fq).bam
+	    }
+	    else {
+                READ_TRIMMING_SINGLE_END(input_fastqs)
+                ALIGNMENT_SINGLE_END(READ_TRIMMING_SINGLE_END.out[0], reference)
+                bam_files = ALIGNMENT_SINGLE_END.out
         }
-        COVERAGE_ANALYSIS(preprocessed_bams)
+	if (params.input_ont) {
+	    preprocessed_bams = PRIMER_SOFTCLIP(OPTIMUS_NO_PRIME(input_bams).prediction)
+	}
+	else {
+            BAM_PREPROCESSING(bam_files, reference)
+            preprocessed_bams = BAM_PREPROCESSING.out.preprocessed_bams
+
+            if (primers) {
+                PRIMER_TRIMMING_IVAR(preprocessed_bams, primers)
+                preprocessed_bams = PRIMER_TRIMMING_IVAR.out.trimmed_bam
+            }
+            COVERAGE_ANALYSIS(preprocessed_bams)
 
         // variant calling
         vcfs_to_normalize = null
-        if (!params.skip_bcftools) {
+        if (!params.skip_bcftools && !params.input_ont) {
             VARIANT_CALLING_BCFTOOLS(preprocessed_bams, reference)
             vcfs_to_normalize = vcfs_to_normalize == null?
                 VARIANT_CALLING_BCFTOOLS.out : vcfs_to_normalize.concat(VARIANT_CALLING_BCFTOOLS.out)
         }
-        if (!params.skip_lofreq) {
+        if (!params.skip_lofreq && !params.input_ont) {
             VARIANT_CALLING_LOFREQ(preprocessed_bams, reference)
             vcfs_to_normalize = vcfs_to_normalize == null?
                 VARIANT_CALLING_LOFREQ.out : vcfs_to_normalize.concat(VARIANT_CALLING_LOFREQ.out)
         }
-        if (!params.skip_gatk) {
+        if (!params.skip_gatk && !params.input_ont) {
             VARIANT_CALLING_GATK(preprocessed_bams, reference)
             vcfs_to_normalize = vcfs_to_normalize == null?
                 VARIANT_CALLING_GATK.out : vcfs_to_normalize.concat(VARIANT_CALLING_GATK.out)
         }
-        if (!params.skip_ivar && gff) {
+        if (!params.skip_ivar && gff && !params.input_ont) {
             VARIANT_CALLING_IVAR(preprocessed_bams, reference, gff)
             IVAR2VCF(VARIANT_CALLING_IVAR.out, reference)
             vcfs_to_normalize = vcfs_to_normalize == null?
                 IVAR2VCF.out : vcfs_to_normalize.concat(IVAR2VCF.out)
         }
+	
     }
     else if (input_fastas) {
         if (!params.skip_pangolin) {
@@ -313,6 +333,10 @@ workflow {
     }
 
     if (preprocessed_bams) {
+        if (params.input_ont) {
+	    CLAIR3(preprocessed_bams.bam)
+	    NANOCALLER(preprocessed_bams.bam)
+	}
         // we can only add technical annotations when we have the reads
         VAFATOR(normalized_vcfs.combine(preprocessed_bams, by: 0))
         VARIANT_VAF_ANNOTATION(VAFATOR.out.annotated_vcf)
diff --git a/modules/13_ont_annotate.nf b/modules/13_ont_annotate.nf
deleted file mode 100755
index 63b32b1..0000000
--- a/modules/13_ont_annotate.nf
+++ /dev/null
@@ -1,169 +0,0 @@
-process VAFATOR {
-    cpus 1
-    memory "3 GB"
-	tag "${sampleId}"
-	publishDir "${params.outDir}/${sampleId}/variant_calls/${caller}", mode: "copy"	
-
-	conda (params.enable_conda ? "bioconda::vafator=1.2.5" : null)
-
-	input:
-	tuple val(sampleId), path(bam), path(bai), path(vcf), val(caller)
-	
-	output:
-	tuple val(sampleId), path("${sampleId}_${caller}_vaf.vcf"), val(caller), emit: annotated_vcf
-
-	script:
-	mq_param = params.vafator_min_mapping_quality != false ? "--mapping-quality " + params.vafator_min_mapping_quality : ""
-	bq_param = params.vafator_min_base_quality != false ? "--base-call-quality " + params.vafator_min_base_quality : ""
-	"""
-	vafator \
-	--input-vcf ${vcf} \
-	--output-vcf ${sampleId}_${caller}_vaf.vcf \
-	--bam vafator ${bam} ${mq_param} ${bq_param}
-	"""
-}
-
-process SNPEFF {
-    cpus 1
-    memory params.memory
-	publishDir "${params.outDir}/${sampleId}/variant_calls/${caller}", mode: "copy"
-	tag "${sampleId}"
-
-	conda (params.enable_conda ? "bioconda::snpeff=5.0 bioconda::samtools=1.16.1" : null)
-
-	input:
-	tuple val(sampleId), path(vcf), val(caller)
-	val(snpeff_data)
-	val(snpeff_config)
-	val(snpeff_organism)
-
-	output:
-	tuple val(sampleId), path("${sampleId}_${caller}_snpeff.vcf.gz"), emit: annotated_vcf
-	path("${sampleId}_${caller}_snpeff.vcf.gz.tbi")
-
-	"""
-	# for some reason the snpEff.config file needs to be in the folder where snpeff runs...
-	cp ${snpeff_config} .
-
-	snpEff eff -Xmx${params.memory} -dataDir ${snpeff_data} \
-	-noStats -no-downstream -no-upstream -no-intergenic -no-intron -onlyProtein -hgvs1LetterAa -noShiftHgvs \
-	${snpeff_organism} ${vcf} | bgzip -c > ${sampleId}_${caller}_snpeff.vcf.gz
-
-	tabix -p vcf ${sampleId}_${caller}_snpeff.vcf.gz
-	"""
-}
-
-
-process VARIANT_VAF_ANNOTATION {
-	cpus 1
-	memory "3 GB"
-	publishDir "${params.outDir}", mode: "copy"
-	tag "${sampleId}"
-
-	conda (params.enable_conda ? "conda-forge::gsl=2.7 bioconda::bcftools=1.14" : null)
-
-	input:
-		tuple val(sampleId), path(vcf)
-
-	output:
-		tuple val(sampleId), path("${sampleId}.lowfreq_subclonal.vcf"), emit: vaf_annotated
-
-	"""
-	tabix -p vcf ${vcf}
-
-	# annotates low frequency and subclonal variants
-	bcftools view -Ob ${vcf} | \
-	bcftools filter \
-	--exclude 'INFO/vafator_af < ${params.low_frequency_variant_threshold}' \
-	--soft-filter LOW_FREQUENCY - | \
-	bcftools filter \
-	--exclude 'INFO/vafator_af >= ${params.low_frequency_variant_threshold} && INFO/vafator_af < ${params.subclonal_variant_threshold}' \
-	--soft-filter SUBCLONAL \
-	--output-type v - | \
-	bcftools filter \
-	--exclude 'INFO/vafator_af >= ${params.subclonal_variant_threshold} && INFO/vafator_af < ${params.lq_clonal_variant_threshold}' \
-	--soft-filter LOW_QUALITY_CLONAL \
-	--output-type v - > ${sampleId}.lowfreq_subclonal.vcf
-	"""
-}
-
-/**
-Add SARS-CoV-2 specific annotations: conservation, Pfam domains and problematic sites.
-Also, according to problematic sites described in DeMaio et al. (2020) we filter out any variants at the beginning and
-end of the genome.
-*/
-process VARIANT_SARSCOV2_ANNOTATION {
-	cpus 1
-	memory "3 GB"
-	publishDir "${params.output}", mode: "copy"
-	tag "${sampleId}"
-
-	conda (params.enable_conda ? "conda-forge::gsl=2.7 bioconda::bcftools=1.14" : null)
-
-	input:
-	tuple val(sampleId), path(vcf)
-
-	output:
-	tuple val(sampleId), path("${sampleId}.annotated_sarscov2.vcf"), emit: annotated_vcfs
-
-	"""
-	bcftools annotate \
-	--annotations ${params.conservation_sarscov2} \
-	--header-lines ${params.conservation_sarscov2_header} \
-	-c CHROM,FROM,TO,CONS_HMM_SARS_COV_2 \
-	--output-type z ${vcf} | \
-	bcftools annotate \
-	--annotations ${params.conservation_sarbecovirus} \
-	--header-lines ${params.conservation_sarbecovirus_header} \
-	-c CHROM,FROM,TO,CONS_HMM_SARBECOVIRUS \
-	--output-type z - | \
-	bcftools annotate \
-	--annotations ${params.conservation_vertebrate} \
-	--header-lines ${params.conservation_vertebrate_header} \
-	-c CHROM,FROM,TO,CONS_HMM_VERTEBRATE_COV \
-	--output-type z - | \
-	bcftools annotate \
-	--annotations ${params.pfam_names} \
-	--header-lines ${params.pfam_names_header} \
-	-c CHROM,FROM,TO,PFAM_NAME \
-	--output-type z - | \
-	bcftools annotate \
-	--annotations ${params.pfam_descriptions} \
-	--header-lines ${params.pfam_descriptions_header} \
-	-c CHROM,FROM,TO,PFAM_DESCRIPTION - | \
-	bcftools filter \
-	--exclude 'POS <= 55 | POS >= 29804' \
-	--output-type z - > annotated_sarscov2.vcf.gz
-
-	tabix -p vcf annotated_sarscov2.vcf.gz
-
-	bcftools annotate \
-	--annotations ${params.problematic_sites} \
-	--columns INFO/problematic:=FILTER annotated_sarscov2.vcf.gz > ${sampleId}.annotated_sarscov2.vcf
-	"""
-}
-
-process PANGOLIN {
-    cpus 1
-    memory "3 GB"
-	publishDir "${params.outDir}", mode: "copy"
-	tag "${sampleId}"
-
-	conda (params.enable_conda ? "bioconda::pangolin=4.1.2" : null)
-
-	input:
-	tuple val(sampleId), path(fasta)
-
-	output:
-	tuple val(name), path("*pangolin.csv")
-
-    """
-    mkdir tmp
-    #--decompress-model
-    pangolin \
-    ${fasta} \
-    --outfile ${sampleId}.pangolin.csv \
-    --tempdir ./tmp \
-    --threads 1
-    """
-}
\ No newline at end of file