diff --git a/conf/hicstuff.config b/conf/hicstuff.config
deleted file mode 100644
index 55f6a237b70f04dca2f026b5e272bb42369cfec3..0000000000000000000000000000000000000000
--- a/conf/hicstuff.config
+++ /dev/null
@@ -1,402 +0,0 @@
-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 = '${params.outdir}'
- tracedir = "${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/${params.custom_config_version}"
- config_profile_description = null
- config_profile_contact = null
- config_profile_url = null
- config_profile_name = null
-
-
- // Max resource options
- // Defaults only, expecting to be overwritten
- max_memory = '128.GB'
- max_cpus = 16
- max_time = '240.h'
-
- // Hicstuff
- hicstuff_bwt2_align_opts = '--very-sensitive-local'
- hicstuff_min_size = 0
- hicstuff_circular = 'false'
- hicstuff_output_contigs = 'info_contigs.txt'
- hicstuff_output_frags = 'fragments_list.txt'
- hicstuff_frags_plot = 'false'
- hicstuff_frags_plot_path = 'frags_hist.pdf'
- hicstuff_valid_pairs = 'valid.pairs'
- hicstuff_valid_idx = 'valid_idx.pairs'
- hicstuff_min_qual = 30
- hicstuff_matrix = 'abs_fragments_contacts_weighted.txt'
- hicstuff_bin = 10000
- hicstuff_valid_idx_filtered = 'valid_idx_filtered.pairs'
- hicstuff_plot_events = 'false'
- hicstuff_pie_plot = 'distrib'
- hicstuff_dist_plot = 'dist'
- hicstuff_centro_file = 'None' //give absolute path or 'None'
- hicstuff_base = 1.1
- hicstuff_distance_out_file = 'distance_law.txt'
- hicstuff_rm_centro = 'None' //int or 'None'
- hicstuff_distance_plot = 'false'
- hicstuff_distance_out_plot = 'plot_distance_law.pdf'
- hicstuff_filter_pcr_out_file = 'valid_idx_pcrfree.pairs'
-
- //Hicstuff optional modules
- filter_event = false
- distance_law = false
- filter_pcr = false
- filter_pcr_picard = true
-
- workflow = 'hicstuff'
-}
-
-process {
- //Default
- publishDir = [
- path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
- mode: 'copy',
- saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
- ]
-
- withName: 'BOWTIE2_ALIGNMENT' {
- ext.prefix = { "${meta.id}_${meta.chunk}_${meta.mates}" }
- ext.args = params.hicstuff_bwt2_align_opts
- publishDir = [
- path: { "${params.outdir}/hicstuff/reads"},
- mode: 'copy'
- ]
- }
-
- withName: 'FRAGMENT_ENZYME' {
- ext.args = { [
- " -m ${params.hicstuff_min_size}",
- " -c ${params.hicstuff_circular}",
- " -o ${params.hicstuff_output_contigs}",
- " -f ${params.hicstuff_output_frags}",
- " -p ${params.hicstuff_frags_plot}",
- " -g ${params.hicstuff_frags_plot_path}"
- ].join('').trim() }
- publishDir = [
- path: { "${params.outdir}/hicstuff/fragment_enzyme" },
- mode: 'copy'
- ]
- }
-
- withName: 'BAM2PAIRS' {
- ext.pairs = params.hicstuff_valid_pairs
- ext.index = params.hicstuff_valid_idx
- ext.args = { [
- " -q ${params.hicstuff_min_qual}",
- " -c ${params.hicstuff_circular}"
- ].join('').trim() }
- publishDir = [
- path: { "${params.outdir}/hicstuff/pairs" },
- mode: 'copy'
- ]
- }
-
- withName: 'FILTER_EVENT' {
- ext.args = { [
- " -o ${params.hicstuff_valid_idx_filtered}",
- " --plot ${params.hicstuff_plot_events}",
- " -d ${params.hicstuff_dist_plot}",
- " -q ${params.hicstuff_pie_plot}"
- ].join('').trim() }
- publishDir = [
- path: { "${params.outdir}/hicstuff/pairs" },
- mode: 'copy'
- ]
- }
-
- withName: 'DISTANCE_LAW' {
- ext.args = { [
- " -c ${params.hicstuff_centro_file}",
- " -b ${params.hicstuff_base}",
- " -o ${params.hicstuff_distance_out_file}",
- " -u ${params.hicstuff_circular}",
- " -r ${params.hicstuff_rm_centro}",
- " -l ${params.hicstuff_distance_plot}",
- " -d ${params.hicstuff_distance_out_plot}"
- ].join('').trim() }
- publishDir = [
- path: { "${params.outdir}/hicstuff/pairs" },
- mode: 'copy'
- ]
- }
-
- withName: 'FILTER_PCR' {
- ext.args = { [
- "-o ${params.hicstuff_filter_pcr_out_file}"
- ].join('').trim() }
- publishDir = [
- path: { "${params.outdir}/hicstuff/pairs" },
- mode: 'copy'
- ]
- }
-
- withName: 'GATK4_MARKDUPLICATES' {
- ext.prefix = { "${meta.id}_${meta.chunk}_${meta.mates}.bam" }
- ext.args = { [
- "--REMOVE_DUPLICATES true"
- ].join('').trim() }
- publishDir = [
- path: { "${params.outdir}/gatk4/bam" },
- mode: 'copy'
- ]
- }
-
- withName: 'PICARD_MARKDUPLICATES' {
- ext.prefix = { "${meta.id}_${meta.chunk}_${meta.mates}" }
- ext.args = { [
- "--REMOVE_DUPLICATES true"
- ].join('').trim() }
- publishDir = [
- path: { "${params.outdir}/picard/bam" },
- mode: 'copy'
- ]
- }
-
- withName: 'SAMTOOLS_SORT' {
- ext.prefix = { "${meta.id}_${meta.chunk}_${meta.mates}_sorted" }
- ext.args = { [
- ""
- ].join('').trim() }
- }
-
- withName: 'SAMTOOLS_SORT_N' {
- ext.prefix = { "${meta.id}_${meta.chunk}_${meta.mates}_nsorted" }
- ext.args = { [
- "-n"
- ].join('').trim() }
- publishDir = [
- path: { "${params.outdir}/gatk4/bam" },
- mode: 'copy'
- ]
- }
-
- withName: 'SAMTOOLS_INDEX' {
- ext.args = { [
- ""
- ].join('').trim() }
- }
-
- withName: 'BUILD_MATRIX' {
- ext.args = params.hicstuff_matrix
- publishDir = [
- path: { "${params.outdir}/hicstuff/matrix" },
- mode: 'copy'
- ]
- }
- withName: 'BUILD_MATRIX_COOL' {
- ext.args = params.hicstuff_matrix
- publishDir = [
- path: { "${params.outdir}/hicstuff/matrix" },
- mode: 'copy'
- ]
- }
- withName: 'BUILD_MATRIX_COOL_ALT' {
- ext.outname = params.hicstuff_matrix
- ext.bin = params.hicstuff_bin
- ext.args = {"-c1 2 -p1 3 -p2 4 -c2 5"}
- publishDir = [
- path: { "${params.outdir}/hicstuff/matrix" },
- mode: 'copy'
- ]
- }
-
- //**********************************************
- // PREPARE_GENOME
- withName: 'BOWTIE2_BUILD' {
- publishDir = [
- path: { "${params.outdir}/genome/bowtie2_index" },
- mode: 'copy'
- ]
- }
-
- withName: 'CUSTOM_GETCHROMSIZES' {
- publishDir = [
- path: { "${params.outdir}/genome" },
- mode: 'copy'
- ]
- }
-
- withName: 'GET_RESTRICTION_FRAGMENTS' {
- publishDir = [
- path: { "${params.outdir}/genome" },
- mode: 'copy'
- ]
- }
-
-}
-
-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.registry = 'quay.io'
- 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' }
-}
-includeConfig 'base.config'
diff --git a/main.nf b/main.nf
index 942feda8495cb7decfaafdb3d01163461d4cbab9..82aaf0f200b77db6710472f821c715376d2e5668 100644
--- a/main.nf
+++ b/main.nf
@@ -35,18 +35,12 @@ WorkflowMain.initialise(workflow, params, log)
*/
include { HIC } from './workflows/hic'
-include { HICSTUFF } from './workflows/hicstuff'
//
// WORKFLOW: Run main nf-core/hic analysis pipeline
//
workflow NFCORE_HIC {
- if (params.workflow == "hicpro" ){
- HIC ()
- }
- else if ( params.workflow == "hicstuff") {
- HICSTUFF ()
- }
+ HIC ()
}
/*
diff --git a/subworkflows/local/hicstuff_sub.nf b/subworkflows/local/hicstuff.nf
similarity index 97%
rename from subworkflows/local/hicstuff_sub.nf
rename to subworkflows/local/hicstuff.nf
index b3070d5bfa2726b7683d3cb5d2bed1d266072613..d9c60abaaa47d6d04750c7072305497bcd384367 100644
--- a/subworkflows/local/hicstuff_sub.nf
+++ b/subworkflows/local/hicstuff.nf
@@ -31,7 +31,7 @@ def singleToPair(row){
return [ meta, row[1] ]
}
-workflow HICSTUFF_SUB {
+workflow HICSTUFF {
take:
reads
@@ -128,7 +128,6 @@ workflow HICSTUFF_SUB {
ch_idx_pairs
)
- HIC_PLOT_MATRIX(
- BUILD_MATRIX_COOL_ALT.out.matrix
- )
+ emit:
+ cool = BUILD_MATRIX_COOL_ALT.out.matrix
}
diff --git a/workflows/hic.nf b/workflows/hic.nf
index 67ccd439ba8a57240f7a70fe08238043c852883f..70c1f8d671574d8da3aadd6710e41fe9eabd7164 100644
--- a/workflows/hic.nf
+++ b/workflows/hic.nf
@@ -109,6 +109,7 @@ include { MULTIQC } from '../modules/local/multiqc'
//
include { INPUT_CHECK } from '../subworkflows/local/input_check'
include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome'
+include { HICSTUFF } from '../subworkflows/local/hicstuff'
include { HICPRO } from '../subworkflows/local/hicpro'
include { COOLER } from '../subworkflows/local/cooler'
include { COMPARTMENTS } from '../subworkflows/local/compartments'
@@ -177,17 +178,18 @@ workflow HIC {
//
// SUB-WORFLOW: HiC-Pro
//
- INPUT_CHECK.out.reads.view()
- HICPRO (
- INPUT_CHECK.out.reads,
- PREPARE_GENOME.out.index,
- PREPARE_GENOME.out.res_frag,
- PREPARE_GENOME.out.chromosome_size,
- ch_ligation_site,
- ch_map_res,
- ch_fasta
- )
- ch_versions = ch_versions.mix(HICPRO.out.versions)
+ if (params.workflow == "hicpro"){
+ HICPRO (
+ INPUT_CHECK.out.reads,
+ PREPARE_GENOME.out.index,
+ PREPARE_GENOME.out.res_frag,
+ PREPARE_GENOME.out.chromosome_size,
+ ch_ligation_site,
+ ch_map_res,
+ ch_fasta
+ )
+ ch_mqc = HICPRO.out.mqc
+ ch_versions = ch_versions.mix(HICPRO.out.versions)
//
// SUB-WORKFLOW: COOLER
@@ -214,13 +216,28 @@ workflow HIC {
)
ch_versions = ch_versions.mix(HIC_PLOT_DIST_VS_COUNTS.out.versions)
}
+ ch_cool = COOLER.out.cool
+}
+
+ else {
+ HICSTUFF(
+ INPUT_CHECK.out.reads,
+ PREPARE_GENOME.out.index,
+ ch_ligation_site,
+ params.digestion, //str enzyme
+ ch_fasta,
+ PREPARE_GENOME.out.chromosome_size
+ )
+ ch_cool = HICSTUFF.out.cool
+ ch_mqc = Channel.empty()
+ }
//
// MODULE: HICEXPLORER/HIC_PLOT_MATRIX
//
if (!params.skip_plot_matrix){
HIC_PLOT_MATRIX(
- COOLER.out.cool
+ ch_cool
)
ch_versions = ch_versions.mix(HIC_PLOT_MATRIX.out.versions)
}
@@ -229,7 +246,7 @@ workflow HIC {
// SUB-WORKFLOW: COMPARTMENT CALLING
//
if (!params.skip_compartments){
- COOLER.out.cool
+ ch_cool
.combine(ch_comp_res)
.filter{ it[0].resolution == it[2] }
.map { it -> [it[0], it[1], it[2]]}
@@ -247,7 +264,7 @@ workflow HIC {
// SUB-WORKFLOW : TADS CALLING
//
if (!params.skip_tads){
- COOLER.out.cool
+ ch_cool
.combine(ch_tads_res)
.filter{ it[0].resolution == it[2] }
.map { it -> [it[0], it[1]]}
@@ -277,14 +294,14 @@ workflow HIC {
ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.map{it->it[1]})
- ch_multiqc_files = ch_multiqc_files.mix(HICPRO.out.mqc)
+ ch_multiqc_files = ch_multiqc_files.mix(ch_mqc)
MULTIQC (
ch_multiqc_config,
ch_multiqc_custom_config.collect().ifEmpty([]),
ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'),
FASTQC.out.zip.map{it->it[1]},
- HICPRO.out.mqc.collect()
+ ch_mqc.collect()
)
multiqc_report = MULTIQC.out.report.toList()
}
diff --git a/workflows/hicstuff.nf b/workflows/hicstuff.nf
deleted file mode 100644
index 8263bd3db82361774f74c84884e373cdc8d51a7c..0000000000000000000000000000000000000000
--- a/workflows/hicstuff.nf
+++ /dev/null
@@ -1,45 +0,0 @@
-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) //str seq avec ^ pour cut
- ligation_site = params.digestion ? params.digest[ params.digestion ].ligation_site ?: false : false
- ch_ligation_site = Channel.value(ligation_site) //str seq
-}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 { HICSTUFF_SUB } from '../subworkflows/local/hicstuff_sub'
-
-workflow HICSTUFF {
- INPUT_CHECK (
- ch_input
- )
- PREPARE_GENOME(
- ch_fasta,
- ch_restriction_site
- )
- HICSTUFF_SUB(
- INPUT_CHECK.out.reads,
- PREPARE_GENOME.out.index,
- ch_ligation_site,
- params.digestion, //str enzyme
- ch_fasta,
- PREPARE_GENOME.out.chromosome_size
- )
-}