diff --git a/conf/hicstuff.config b/conf/hicstuff.config
new file mode 100644
index 0000000000000000000000000000000000000000..4af147d2f872f71614a12f459b9fab242ab514e4
--- /dev/null
+++ b/conf/hicstuff.config
@@ -0,0 +1,197 @@
+process {
+ //Default
+ publishDir = [
+ path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+ mode: 'copy',
+ saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+ ]
+}
+
+params {
+
+ // Input options
+ input = null
+
+
+ // References
+ genome = null
+ igenomes_base = 's3://ngi-igenomes/igenomes'
+ igenomes_ignore = false
+ chromosome_size = null
+ restriction_fragments = null
+ save_reference = false
+
+ // Mapping
+ split_fastq = false
+ fastq_chunks_size = 20000000
+ save_interaction_bam = false
+ save_aligned_intermediates = false
+ bwt2_opts_end2end = '--very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder'
+ bwt2_opts_trimmed = '--very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder'
+ keep_dups = false
+ keep_multi = false
+ min_mapq = 10
+
+ // Digestion Hi-C
+ digestion = null
+ ligation_site = null
+ restriction_site = null
+ digest {
+ 'hindiii'{
+ restriction_site='A^AGCTT'
+ ligation_site='AAGCTAGCTT'
+ }
+ 'mboi' {
+ restriction_site='^GATC'
+ ligation_site='GATCGATC'
+ }
+ 'dpnii' {
+ restriction_site='^GATC'
+ ligation_site='GATCGATC'
+ }
+ 'arima' {
+ restriction_site='^GATC,G^ANTC'
+ ligation_site='GATCGATC,GATCANTC,GANTGATC,GANTANTC'
+ }
+ }
+
+ min_restriction_fragment_size = 0
+ max_restriction_fragment_size = 0
+ min_insert_size = 0
+ max_insert_size = 0
+ save_pairs_intermediates = false
+
+ // Dnase Hi-C
+ dnase = false
+ min_cis_dist = 0
+
+ // Contact maps
+ save_raw_maps = false
+ bin_size = '1000000'
+ res_zoomify = null
+ hicpro_maps = false
+ ice_max_iter = 100
+ ice_filter_low_count_perc = 0.02
+ ice_filter_high_count_perc = 0
+ ice_eps = 0.1
+
+ // Downstream Analysis
+ res_dist_decay = '250000'
+ tads_caller = 'insulation'
+ res_tads = '40000'
+ res_compartments = '250000'
+
+ // Workflow
+ skip_maps = false
+ skip_balancing = false
+ skip_mcool = false
+ skip_dist_decay = false
+ skip_compartments = false
+ skip_tads = false
+ skip_multiqc = false
+
+ // MultiQC options
+ multiqc_config = null
+ multiqc_title = null
+ multiqc_logo = null
+ max_multiqc_email_size = '25.MB'
+ multiqc_methods_description = null
+
+ // Boilerplate options
+ outdir = './results'
+ tracedir = "${params.outdir}/pipeline_info"
+ publish_dir_mode = 'copy'
+ email = null
+ email_on_fail = null
+ plaintext_email = false
+ monochrome_logs = false
+ hook_url = null
+ help = false
+ version = false
+ validate_params = true
+ show_hidden_params = false
+ schema_ignore_params = 'genomes,digest'
+
+ // Config options
+ custom_config_version = 'master'
+ custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
+ config_profile_description = null
+ config_profile_contact = null
+ config_profile_url = null
+ config_profile_name = null
+
+
+ // Max resource options
+ // Defaults only, expecting to be overwritten
+ max_memory = '128.GB'
+ max_cpus = 16
+ max_time = '240.h'
+
+}
+profiles {
+ debug { process.beforeScript = 'echo $HOSTNAME' }
+ conda {
+ conda.enabled = true
+ docker.enabled = false
+ singularity.enabled = false
+ podman.enabled = false
+ shifter.enabled = false
+ charliecloud.enabled = false
+ }
+ mamba {
+ conda.enabled = true
+ conda.useMamba = true
+ docker.enabled = false
+ singularity.enabled = false
+ podman.enabled = false
+ shifter.enabled = false
+ charliecloud.enabled = false
+ }
+ docker {
+ docker.enabled = true
+ docker.userEmulation = true
+ singularity.enabled = false
+ podman.enabled = false
+ shifter.enabled = false
+ charliecloud.enabled = false
+ }
+ arm {
+ docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
+ }
+ singularity {
+ singularity.enabled = true
+ singularity.autoMounts = true
+ docker.enabled = false
+ podman.enabled = false
+ shifter.enabled = false
+ charliecloud.enabled = false
+ }
+ podman {
+ podman.enabled = true
+ docker.enabled = false
+ singularity.enabled = false
+ shifter.enabled = false
+ charliecloud.enabled = false
+ }
+ shifter {
+ shifter.enabled = true
+ docker.enabled = false
+ singularity.enabled = false
+ podman.enabled = false
+ charliecloud.enabled = false
+ }
+ charliecloud {
+ charliecloud.enabled = true
+ docker.enabled = false
+ singularity.enabled = false
+ podman.enabled = false
+ shifter.enabled = false
+ }
+ gitpod {
+ executor.name = 'local'
+ executor.cpus = 16
+ executor.memory = 60.GB
+ }
+ test { includeConfig 'conf/test.config' }
+ test_full { includeConfig 'conf/test_full.config' }
+}
diff --git a/modules/local/hicstuff/align_bowtie2.nf b/modules/local/hicstuff/align_bowtie2.nf
new file mode 100644
index 0000000000000000000000000000000000000000..a3f2f1c237d0c66d5a46cf13900c7193176cf12a
--- /dev/null
+++ b/modules/local/hicstuff/align_bowtie2.nf
@@ -0,0 +1,30 @@
+process BOWTIE2_ALIGNMENT {
+ tag "$meta.id"
+ label "process_high"
+
+ conda "bioconda::bowtie2=2.4.4 bioconda::samtools=1.16.1 conda-forge::pigz=2.6"
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' :
+ 'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' }"
+
+ input:
+ tuple val(meta), path(reads)
+ tuple val(meta2), path(index)
+
+ output:
+ tuple val(meta), path ("*.bam"), emit: bam
+
+ script:
+ def prefix = task.ext.prefix ?: "${meta.id}"
+
+ """
+ INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/\\.rev.1.bt2\$//"`
+ [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed "s/\\.rev.1.bt2l\$//"`
+ [ -z "\$INDEX" ] && echo "Bowtie2 index files not found" 1>&2 && exit 1
+
+ bowtie2 --very-sensitive-local -p $task.cpus -x \$INDEX -U $reads > ${prefix}.tmp
+
+ samtools view -F 2048 -h -@ $task.cpus ${prefix}.tmp | samtools sort -n -@ $task.cpus -o ${prefix}.bam -
+ """
+
+}
diff --git a/test.nf b/test.nf
new file mode 100644
index 0000000000000000000000000000000000000000..b960e23168f81ba91048847de68419281d891640
--- /dev/null
+++ b/test.nf
@@ -0,0 +1,55 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ GENOME PARAMETER VALUES
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
+params.bwt2_index = WorkflowMain.getGenomeAttribute(params, 'bowtie2')
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ VALIDATE & PRINT PARAMETER SUMMARY
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+WorkflowMain.initialise(workflow, params, log)
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ NAMED WORKFLOW FOR PIPELINE
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+include { HICSTUFF } from './workflows/hicstuff'
+
+//
+// WORKFLOW: Run main nf-core/hic analysis pipeline
+//
+workflow TEST_HICSTUFF {
+ HICSTUFF ()
+}
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ RUN ALL WORKFLOWS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+//
+// WORKFLOW: Execute a single named workflow for the pipeline
+// See: https://github.com/nf-core/rnaseq/issues/619
+//
+workflow {
+ TEST_HICSTUFF ()
+}
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ THE END
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
diff --git a/workflows/hicstuff.nf b/workflows/hicstuff.nf
new file mode 100644
index 0000000000000000000000000000000000000000..e411e18bb2154413149ec78c64d2ceed92b87e3c
--- /dev/null
+++ b/workflows/hicstuff.nf
@@ -0,0 +1,41 @@
+def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
+// Validate input parameters
+WorkflowHic.initialise(params, log)
+// Check mandatory parameters
+if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
+// Digestion parameters
+if (params.digestion){
+ restriction_site = params.digestion ? params.digest[ params.digestion ].restriction_site ?: false : false
+ ch_restriction_site = Channel.value(restriction_site)
+ ligation_site = params.digestion ? params.digest[ params.digestion ].ligation_site ?: false : false
+ ch_ligation_site = Channel.value(ligation_site)
+}else if (params.dnase){
+ ch_restriction_site = Channel.empty()
+ ch_ligation_site = Channel.empty()
+}else{
+ exit 1, "Ligation motif not found. Please either use the `--digestion` parameters or specify the `--restriction_site` and `--ligation_site`. For DNase Hi-C, please use '--dnase' option"
+}
+
+Channel.fromPath( params.fasta )
+ .ifEmpty { exit 1, "Genome index: Fasta file not found: ${params.fasta}" }
+ .map{it->[[:],it]}
+ .set { ch_fasta }
+
+
+include { INPUT_CHECK } from '../subworkflows/local/input_check'
+include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome'
+include { BOWTIE2_ALIGNMENT } from '../modules/local/hicstuff/align_bowtie2'
+
+workflow HICSTUFF {
+ INPUT_CHECK (
+ ch_input
+ )
+ PREPARE_GENOME(
+ ch_fasta,
+ ch_restriction_site
+ )
+ BOWTIE2_ALIGNMENT(
+ INPUT_CHECK.out.reads,
+ PREPARE_GENOME.out.index
+ )
+}