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main.nf
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#!/usr/bin/env nextflow
/*
========================================================================================
nf-core/hic
========================================================================================
nf-core/hic Analysis Pipeline.
#### Homepage / Documentation
https://github.com/nf-core/hic
----------------------------------------------------------------------------------------
*/
log.info Headers.nf_core(workflow, params.monochrome_logs)
////////////////////////////////////////////////////
/* -- PRINT HELP -- */
////////////////////////////////////////////////////+
def json_schema = "$projectDir/nextflow_schema.json"
if (params.help) {
def command = "nextflow run nf-core/hic --input '*_R{1,2}.fastq.gz' -profile docker"
log.info NfcoreSchema.params_help(workflow, params, json_schema, command)
exit 0
}
////////////////////////////////////////////////////
/* -- VALIDATE PARAMETERS -- */
////////////////////////////////////////////////////+
if (params.validate_params) {
NfcoreSchema.validateParameters(params, json_schema, log)
}
// Check if genome exists in the config file
if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
exit 1, "The provided genome '${params.genome}' is not available in the iGenomes file. Currently the available genomes are ${params.genomes.keySet().join(', ')}"
}
if (params.digest && params.digestion && !params.digest.containsKey(params.digestion)) {
exit 1, "Unknown digestion protocol. Currently, the available digestion options are ${params.digest.keySet().join(", ")}. Please set manually the '--restriction_site' and '--ligation_site' parameters."
}
params.restriction_site = params.digestion ? params.digest[ params.digestion ].restriction_site ?: false : false
params.ligation_site = params.digestion ? params.digest[ params.digestion ].ligation_site ?: false : false
// Check Digestion or DNase Hi-C mode
if (!params.dnase && !params.ligation_site) {
exit 1, "Ligation motif not found. Please either use the `--digestion` parameters or specify the `--restriction_site` and `--ligation_site`. For DNase Hi-C, please use '--dnase' option"
}
// Reference index path configuration
params.bwt2_index = params.genome ? params.genomes[ params.genome ].bowtie2 ?: false : false
params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
////////////////////////////////////////////////////
/* -- Collect configuration parameters -- */
////////////////////////////////////////////////////
// Check AWS batch settings
if (workflow.profile.contains('awsbatch')) {
// AWSBatch sanity checking
if (!params.awsqueue || !params.awsregion) exit 1, 'Specify correct --awsqueue and --awsregion parameters on AWSBatch!'
// Check outdir paths to be S3 buckets if running on AWSBatch
// related: https://github.com/nextflow-io/nextflow/issues/813
if (!params.outdir.startsWith('s3:')) exit 1, 'Outdir not on S3 - specify S3 Bucket to run on AWSBatch!'
// Prevent trace files to be stored on S3 since S3 does not support rolling files.
if (params.tracedir.startsWith('s3:')) exit 1, 'Specify a local tracedir or run without trace! S3 cannot be used for tracefiles.'
}
// Stage config files
ch_multiqc_config = file("$projectDir/assets/multiqc_config.yaml", checkIfExists: true)
ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
ch_output_docs = file("$projectDir/docs/output.md", checkIfExists: true)
ch_output_docs_images = file("$projectDir/docs/images/", checkIfExists: true)
/*
* input read files
*/
if (params.input_paths){
raw_reads = Channel.create()
raw_reads_2 = Channel.create()
Channel
.from( params.input_paths )
.map { row -> [ row[0], [file(row[1][0]), file(row[1][1])]] }
.separate( raw_reads, raw_reads_2 ) { a -> [tuple(a[0] + "_R1", a[1][0]), tuple(a[0] + "_R2", a[1][1])] }
}else{
raw_reads = Channel.create()
raw_reads_2 = Channel.create()
if ( params.split_fastq ){
Channel
.fromFilePairs( params.input, flat:true )
.splitFastq( by: params.fastq_chunks_size, pe:true, file: true, compress:true)
.separate( raw_reads, raw_reads_2 ) { a -> [tuple(a[0] + "_R1", a[1]), tuple(a[0] + "_R2", a[2])] }
}else{
Channel
.fromFilePairs( params.input )
.separate( raw_reads, raw_reads_2 ) { a -> [tuple(a[0] + "_R1", a[1][0]), tuple(a[0] + "_R2", a[1][1])] }
}
}
// Update sample name if splitFastq is used
def updateSampleName(x) {
if ((matcher = x[1] =~ /\s*(\.[\d]+).fastq.gz/)) {
res = matcher[0][1]
}
return [x[0] + res, x[1]]
}
if (params.split_fastq ){
raw_reads = raw_reads.concat( raw_reads_2 ).map{it -> updateSampleName(it)}.dump(tag:'input')
}else{
raw_reads = raw_reads.concat( raw_reads_2 ).dump(tag:'input')
}
/*
* Other input channels
*/
// Reference genome
if ( params.bwt2_index ){
Channel.fromPath( params.bwt2_index , checkIfExists: true)
.ifEmpty { exit 1, "Genome index: Provided index not found: ${params.bwt2_index}" }
.into { bwt2_index_end2end; bwt2_index_trim }
}
else if ( params.fasta ) {
Channel.fromPath( params.fasta )
.ifEmpty { exit 1, "Genome index: Fasta file not found: ${params.fasta}" }
.into { fasta_for_index }
}
else {
exit 1, "No reference genome specified!"
}
// Chromosome size
if ( params.chromosome_size ){
Channel.fromPath( params.chromosome_size , checkIfExists: true)
.into {chrsize; chrsize_build; chrsize_raw; chrsize_balance; chrsize_zoom; chrsize_compartments}
}
else if ( params.fasta ){
Channel.fromPath( params.fasta )
.ifEmpty { exit 1, "Chromosome sizes: Fasta file not found: ${params.fasta}" }
.set { fasta_for_chromsize }
}
else {
exit 1, "No chromosome size specified!"
}
// Restriction fragments
if ( params.restriction_fragments ){
Channel.fromPath( params.restriction_fragments, checkIfExists: true )
.set {res_frag_file}
}
else if ( params.fasta && params.restriction_site ){
Channel.fromPath( params.fasta )
.ifEmpty { exit 1, "Restriction fragments: Fasta file not found: ${params.fasta}" }
.set { fasta_for_resfrag }
}
else if (! params.dnase) {
exit 1, "No restriction fragments file specified!"
}
// Resolutions for contact maps
map_res = Channel.from( params.bin_size ).splitCsv().flatten()
all_res = params.bin_size
if (params.res_tads && !params.skip_tads){
Channel.from( "${params.res_tads}" )
.splitCsv()
.flatten()
.into {tads_bin; tads_res_hicexplorer; tads_res_insulation}
map_res = map_res.concat(tads_bin)
all_res = all_res + ',' + params.res_tads
}else{
tads_res_hicexplorer=Channel.empty()
tads_res_insulation=Channel.empty()
tads_bin=Channel.empty()
if (!params.skip_tads){
log.warn "[nf-core/hic] Hi-C resolution for TADs calling not specified. See --res_tads"
}
}
if (params.res_dist_decay && !params.skip_dist_decay){
Channel.from( "${params.res_dist_decay}" )
.splitCsv()
.flatten()
.into {ddecay_res; ddecay_bin }
map_res = map_res.concat(ddecay_bin)
all_res = all_res + ',' + params.res_dist_decay
}else{
ddecay_res = Channel.create()
ddecay_bin = Channel.create()
if (!params.skip_dist_decay){
log.warn "[nf-core/hic] Hi-C resolution for distance decay not specified. See --res_dist_decay"
}
}
if (params.res_compartments && !params.skip_compartments){
Channel.fromPath( params.fasta )
.ifEmpty { exit 1, "Compartments calling: Fasta file not found: ${params.fasta}" }
.set { fasta_for_compartments }
Channel.from( "${params.res_compartments}" )
.splitCsv()
.flatten()
.into {comp_bin; comp_res}
map_res = map_res.concat(comp_bin)
all_res = all_res + ',' + params.res_compartments
}else{
fasta_for_compartments = Channel.empty()
comp_res = Channel.create()
if (!params.skip_compartments){
log.warn "[nf-core/hic] Hi-C resolution for compartment calling not specified. See --res_compartments"
}
}
map_res
.unique()
.into { map_res_summary; map_res; map_res_cool; map_comp }
////////////////////////////////////////////////////
/* -- PRINT PARAMETER SUMMARY -- */
////////////////////////////////////////////////////
log.info NfcoreSchema.params_summary_log(workflow, params, json_schema)
// Header log info
def summary = [:]
if (workflow.revision) summary['Pipeline Release'] = workflow.revision
summary['Run Name'] = workflow.runName
summary['Input'] = params.input
summary['splitFastq'] = params.split_fastq
if (params.split_fastq)
summary['Read chunks Size'] = params.fastq_chunks_size
summary['Fasta Ref'] = params.fasta
if (params.restriction_site){
summary['Digestion'] = params.digestion
summary['Restriction Motif']= params.restriction_site
summary['Ligation Motif'] = params.ligation_site
summary['Min Fragment Size']= params.min_restriction_fragment_size
summary['Max Fragment Size']= params.max_restriction_fragment_size
summary['Min Insert Size'] = params.min_insert_size
summary['Max Insert Size'] = params.max_insert_size
}else{
summary['DNase Mode'] = params.dnase
summary['Min CIS dist'] = params.min_cis_dist
}
summary['Min MAPQ'] = params.min_mapq
summary['Keep Duplicates'] = params.keep_dups ? 'Yes' : 'No'
summary['Keep Multihits'] = params.keep_multi ? 'Yes' : 'No'
summary['Maps resolution'] = all_res
summary['Max Resources'] = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job"
if (workflow.containerEngine) summary['Container'] = "$workflow.containerEngine - $workflow.container"
summary['Output dir'] = params.outdir
summary['Launch dir'] = workflow.launchDir
summary['Working dir'] = workflow.workDir
summary['Script dir'] = workflow.projectDir
summary['User'] = workflow.userName
if (workflow.profile.contains('awsbatch')) {
summary['AWS Region'] = params.awsregion
summary['AWS Queue'] = params.awsqueue
summary['AWS CLI'] = params.awscli
}
summary['Config Profile'] = workflow.profile
if (params.config_profile_description) summary['Config Profile Description'] = params.config_profile_description
if (params.config_profile_contact) summary['Config Profile Contact'] = params.config_profile_contact
if (params.config_profile_url) summary['Config Profile URL'] = params.config_profile_url
summary['Config Files'] = workflow.configFiles.join(', ')
if (params.email || params.email_on_fail) {
summary['E-mail Address'] = params.email
summary['E-mail on failure'] = params.email_on_fail
summary['MultiQC maxsize'] = params.max_multiqc_email_size
}
// Check the hostnames against configured profiles
checkHostname()
Channel.from(summary.collect{ [it.key, it.value] })
.map { k,v -> "<dt>$k</dt><dd><samp>${v ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>" }
.reduce { a, b -> return [a, b].join("\n ") }
.map { x -> """
id: 'nf-core-hic-summary'
description: " - this information is collected when the pipeline is started."
section_name: 'nf-core/hic Workflow Summary'
section_href: 'https://github.com/nf-core/hic'
plot_type: 'html'
data: |
<dl class=\"dl-horizontal\">
$x
</dl>
""".stripIndent() }
.set { ch_workflow_summary }
/*
* Parse software version numbers
*/
process get_software_versions {
publishDir "${params.outdir}/pipeline_info", mode: params.publish_dir_mode,
saveAs: { filename -> if (filename.indexOf('.csv') > 0) filename else null }
output:
file 'software_versions_mqc.yaml' into ch_software_versions_yaml
file 'software_versions.csv'
script:
"""
echo $workflow.manifest.version > v_pipeline.txt
echo $workflow.nextflow.version > v_nextflow.txt
bowtie2 --version > v_bowtie2.txt
python --version > v_python.txt 2>&1
samtools --version > v_samtools.txt
multiqc --version > v_multiqc.txt
scrape_software_versions.py &> software_versions_mqc.yaml
"""
}
/****************************************************
* PRE-PROCESSING
*/
if(!params.bwt2_index && params.fasta){
process makeBowtie2Index {
tag "$fasta_base"
label 'process_highmem'
publishDir path: { params.save_reference ? "${params.outdir}/reference_genome" : params.outdir },
saveAs: { params.save_reference ? it : null }, mode: params.publish_dir_mode
input:
file fasta from fasta_for_index
output:
file "bowtie2_index" into bwt2_index_end2end
file "bowtie2_index" into bwt2_index_trim
script:
fasta_base = fasta.toString() - ~/(\.fa)?(\.fasta)?(\.fas)?(\.fsa)?$/
"""
mkdir bowtie2_index
bowtie2-build ${fasta} bowtie2_index/${fasta_base}
"""
}
}
if(!params.chromosome_size && params.fasta){
process makeChromSize {
tag "$fasta"
label 'process_low'
publishDir path: { params.save_reference ? "${params.outdir}/reference_genome" : params.outdir },
saveAs: { params.save_reference ? it : null }, mode: params.publish_dir_mode
input:
file fasta from fasta_for_chromsize
output:
file "*.size" into chrsize, chrsize_build, chrsize_raw, chrsize_balance, chrsize_zoom, chrsize_compartments
script:
"""
samtools faidx ${fasta}
cut -f1,2 ${fasta}.fai > chrom.size
"""
}
}
if(!params.restriction_fragments && params.fasta && !params.dnase){
process getRestrictionFragments {
tag "$fasta ${params.restriction_site}"
label 'process_low'
publishDir path: { params.save_reference ? "${params.outdir}/reference_genome" : params.outdir },
saveAs: { params.save_reference ? it : null }, mode: params.publish_dir_mode
input:
file fasta from fasta_for_resfrag
output:
file "*.bed" into res_frag_file
script:
"""
digest_genome.py -r ${params.restriction_site} -o restriction_fragments.bed ${fasta}
"""
}
}
/****************************************************
* MAIN WORKFLOW
*/
/*
* HiC-pro - Two-steps Reads Mapping
*/
process bowtie2_end_to_end {
tag "$sample"
label 'process_medium'
publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping/bwt2_end2end" : params.outdir },
saveAs: { filename -> if (params.save_aligned_intermediates) filename }, mode: params.publish_dir_mode
input:
set val(sample), file(reads) from raw_reads
file index from bwt2_index_end2end.collect()
output:
set val(sample), file("${prefix}_unmap.fastq") into unmapped_end_to_end
set val(sample), file("${prefix}.bam") into end_to_end_bam
script:
prefix = reads.toString() - ~/(\.fq)?(\.fastq)?(\.gz)?$/
def bwt2_opts = params.bwt2_opts_end2end
if (!params.dnase){
"""
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
bowtie2 --rg-id BMG --rg SM:${prefix} \\
${bwt2_opts} \\
-p ${task.cpus} \\
-x \${INDEX} \\
--un ${prefix}_unmap.fastq \\
-U ${reads} | samtools view -F 4 -bS - > ${prefix}.bam
"""
}else{
"""
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
bowtie2 --rg-id BMG --rg SM:${prefix} \\
${bwt2_opts} \\
-p ${task.cpus} \\
-x \${INDEX} \\
--un ${prefix}_unmap.fastq \\
-U ${reads} > ${prefix}.bam
"""
}
}
process trim_reads {
tag "$sample"
label 'process_low'
publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping/bwt2_trimmed" : params.outdir },
saveAs: { filename -> if (params.save_aligned_intermediates) filename }, mode: params.publish_dir_mode
when:
!params.dnase
input:
set val(sample), file(reads) from unmapped_end_to_end
output:
set val(sample), file("${prefix}_trimmed.fastq") into trimmed_reads
script:
prefix = reads.toString() - ~/(\.fq)?(\.fastq)?(\.gz)?$/
"""
cutsite_trimming --fastq $reads \\
--cutsite ${params.ligation_site} \\
--out ${prefix}_trimmed.fastq
"""
}
process bowtie2_on_trimmed_reads {
tag "$sample"
label 'process_medium'
publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping/bwt2_trimmed" : params.outdir },
saveAs: { filename -> if (params.save_aligned_intermediates) filename }, mode: params.publish_dir_mode
when:
!params.dnase
input:
set val(sample), file(reads) from trimmed_reads
file index from bwt2_index_trim.collect()
output:
set val(sample), file("${prefix}_trimmed.bam") into trimmed_bam
script:
prefix = reads.toString() - ~/(_trimmed)?(\.fq)?(\.fastq)?(\.gz)?$/
"""
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
bowtie2 --rg-id BMG --rg SM:${prefix} \\
${params.bwt2_opts_trimmed} \\
-p ${task.cpus} \\
-x \${INDEX} \\
-U ${reads} | samtools view -bS - > ${prefix}_trimmed.bam
"""
}
if (!params.dnase){
process bowtie2_merge_mapping_steps{
tag "$prefix = $bam1 + $bam2"
label 'process_medium'
publishDir "${params.outdir}/hicpro/mapping", mode: params.publish_dir_mode,
saveAs: { filename -> if (params.save_aligned_intermediates && filename.endsWith("stat")) "stats/$filename"
else if (params.save_aligned_intermediates) filename}
input:
set val(prefix), file(bam1), file(bam2) from end_to_end_bam.join( trimmed_bam ).dump(tag:'merge')
output:
set val(sample), file("${prefix}_bwt2merged.bam") into bwt2_merged_bam
set val(oname), file("${prefix}.mapstat") into all_mapstat
script:
sample = prefix.toString() - ~/(_R1|_R2)/
tag = prefix.toString() =~/_R1/ ? "R1" : "R2"
oname = prefix.toString() - ~/(\.[0-9]+)$/
"""
samtools merge -@ ${task.cpus} \\
-f ${prefix}_bwt2merged.bam \\
${bam1} ${bam2}
samtools sort -@ ${task.cpus} -m 800M \\
-n \\
-o ${prefix}_bwt2merged.sorted.bam \\
${prefix}_bwt2merged.bam
mv ${prefix}_bwt2merged.sorted.bam ${prefix}_bwt2merged.bam
echo "## ${prefix}" > ${prefix}.mapstat
echo -n "total_${tag}\t" >> ${prefix}.mapstat
samtools view -c ${prefix}_bwt2merged.bam >> ${prefix}.mapstat
echo -n "mapped_${tag}\t" >> ${prefix}.mapstat
samtools view -c -F 4 ${prefix}_bwt2merged.bam >> ${prefix}.mapstat
echo -n "global_${tag}\t" >> ${prefix}.mapstat
samtools view -c -F 4 ${bam1} >> ${prefix}.mapstat
echo -n "local_${tag}\t" >> ${prefix}.mapstat
samtools view -c -F 4 ${bam2} >> ${prefix}.mapstat
"""
}
}else{
process dnase_mapping_stats{
tag "$sample = $bam"
label 'process_medium'
publishDir "${params.outdir}/hicpro/mapping", mode: params.publish_dir_mode,
saveAs: { filename -> if (params.save_aligned_intermediates && filename.endsWith("stat")) "stats/$filename"
else if (params.save_aligned_intermediates) filename}
input:
set val(prefix), file(bam) from end_to_end_bam
output:
set val(sample), file(bam) into bwt2_merged_bam
set val(oname), file("${prefix}.mapstat") into all_mapstat
script:
sample = prefix.toString() - ~/(_R1|_R2)/
tag = prefix.toString() =~/_R1/ ? "R1" : "R2"
oname = prefix.toString() - ~/(\.[0-9]+)$/
"""
echo "## ${prefix}" > ${prefix}.mapstat
echo -n "total_${tag}\t" >> ${prefix}.mapstat
samtools view -c ${bam} >> ${prefix}.mapstat
echo -n "mapped_${tag}\t" >> ${prefix}.mapstat
samtools view -c -F 4 ${bam} >> ${prefix}.mapstat
echo -n "global_${tag}\t" >> ${prefix}.mapstat
samtools view -c -F 4 ${bam} >> ${prefix}.mapstat
echo -n "local_${tag}\t0" >> ${prefix}.mapstat
"""
}
}
process combine_mates{
tag "$sample = $r1_prefix + $r2_prefix"
label 'process_low'
publishDir "${params.outdir}/hicpro/mapping", mode: params.publish_dir_mode,
saveAs: {filename -> filename.endsWith(".pairstat") ? "stats/$filename" : "$filename"}
input:
set val(sample), file(aligned_bam) from bwt2_merged_bam.groupTuple()
output:
set val(oname), file("${sample}_bwt2pairs.bam") into paired_bam
set val(oname), file("*.pairstat") into all_pairstat
script:
r1_bam = aligned_bam[0]
r1_prefix = r1_bam.toString() - ~/_bwt2merged.bam$/
r2_bam = aligned_bam[1]
r2_prefix = r2_bam.toString() - ~/_bwt2merged.bam$/
oname = sample.toString() - ~/(\.[0-9]+)$/
def opts = "-t"
if (params.keep_multi) {
opts="${opts} --multi"
}else if (params.min_mapq){
opts="${opts} -q ${params.min_mapq}"
}
"""
mergeSAM.py -f ${r1_bam} -r ${r2_bam} -o ${sample}_bwt2pairs.bam ${opts}
"""
}
/*
* HiC-Pro - detect valid interaction from aligned data
*/
if (!params.dnase){
process get_valid_interaction{
tag "$sample"
label 'process_low'
publishDir "${params.outdir}/hicpro/valid_pairs", mode: params.publish_dir_mode,
saveAs: {filename -> if (filename.endsWith("RSstat")) "stats/$filename"
else if (filename.endsWith(".validPairs")) filename
else if (params.save_nonvalid_pairs) filename}
input:
set val(sample), file(pe_bam) from paired_bam
file frag_file from res_frag_file.collect()
output:
set val(sample), file("*.validPairs") into valid_pairs
set val(sample), file("*.validPairs") into valid_pairs_4cool
set val(sample), file("*.DEPairs") into de_pairs
set val(sample), file("*.SCPairs") into sc_pairs
set val(sample), file("*.REPairs") into re_pairs
set val(sample), file("*.FiltPairs") into filt_pairs
set val(sample), file("*RSstat") into all_rsstat
script:
if (params.split_fastq){
sample = sample.toString() - ~/(\.[0-9]+)$/
}
def opts = ""
opts += params.min_cis_dist > 0 ? " -d ${params.min_cis_dist}" : ''
opts += params.min_insert_size > 0 ? " -s ${params.min_insert_size}" : ''
opts += params.max_insert_size > 0 ? " -l ${params.max_insert_size}" : ''
opts += params.min_restriction_fragment_size > 0 ? " -t ${params.min_restriction_fragment_size}" : ''
opts += params.max_restriction_fragment_size > 0 ? " -m ${params.max_restriction_fragment_size}" : ''
opts += params.save_interaction_bam ? " --sam" : ''
prefix = pe_bam.toString() - ~/.bam/
"""
mapped_2hic_fragments.py -f ${frag_file} -r ${pe_bam} --all ${opts}
sort -k2,2V -k3,3n -k5,5V -k6,6n -o ${prefix}.validPairs ${prefix}.validPairs
"""
}
}
else{
process get_valid_interaction_dnase{
tag "$sample"
label 'process_low'
publishDir "${params.outdir}/hicpro/valid_pairs", mode: params.publish_dir_mode,
saveAs: {filename -> if (filename.endsWith("RSstat")) "stats/$filename"
else filename}
input:
set val(sample), file(pe_bam) from paired_bam
output:
set val(sample), file("*.validPairs") into valid_pairs
set val(sample), file("*.validPairs") into valid_pairs_4cool
set val(sample), file("*RSstat") into all_rsstat
script:
if (params.split_fastq){
sample = sample.toString() - ~/(\.[0-9]+)$/
}
opts = params.min_cis_dist > 0 ? " -d ${params.min_cis_dist}" : ''
prefix = pe_bam.toString() - ~/.bam/
"""
mapped_2hic_dnase.py -r ${pe_bam} ${opts}
sort -k2,2V -k3,3n -k5,5V -k6,6n -o ${prefix}.validPairs ${prefix}.validPairs
"""
}
}
/*
* Remove duplicates
*/
process remove_duplicates {
tag "$sample"
label 'process_highmem'
publishDir "${params.outdir}/hicpro/valid_pairs", mode: params.publish_dir_mode,
saveAs: {filename -> if (filename.endsWith("mergestat")) "stats/$filename"
else if (filename.endsWith("allValidPairs")) "$filename"}
input:
set val(sample), file(vpairs) from valid_pairs.groupTuple()
output:
set val(sample), file("*.allValidPairs") into ch_vpairs, ch_vpairs_cool
file("stats/") into mqc_mergestat
file("*mergestat") into all_mergestat
script:
if ( ! params.keep_dups ){
"""
mkdir -p stats/${sample}
## Sort valid pairs and remove read pairs with same starts (i.e duplicated read pairs)
sort -S 50% -k2,2V -k3,3n -k5,5V -k6,6n -m ${vpairs} | \\
awk -F"\\t" 'BEGIN{c1=0;c2=0;s1=0;s2=0}(c1!=\$2 || c2!=\$5 || s1!=\$3 || s2!=\$6){print;c1=\$2;c2=\$5;s1=\$3;s2=\$6}' > ${sample}.allValidPairs
echo -n "valid_interaction\t" > ${sample}_allValidPairs.mergestat
cat ${vpairs} | wc -l >> ${sample}_allValidPairs.mergestat
echo -n "valid_interaction_rmdup\t" >> ${sample}_allValidPairs.mergestat
cat ${sample}.allValidPairs | wc -l >> ${sample}_allValidPairs.mergestat
## Count short range (<20000) vs long range contacts
awk 'BEGIN{cis=0;trans=0;sr=0;lr=0} \$2 == \$5{cis=cis+1; d=\$6>\$3?\$6-\$3:\$3-\$6; if (d<=20000){sr=sr+1}else{lr=lr+1}} \$2!=\$5{trans=trans+1}END{print "trans_interaction\\t"trans"\\ncis_interaction\\t"cis"\\ncis_shortRange\\t"sr"\\ncis_longRange\\t"lr}' ${sample}.allValidPairs >> ${sample}_allValidPairs.mergestat
## For MultiQC
mkdir -p stats/${sample}
cp ${sample}_allValidPairs.mergestat stats/${sample}/
"""
}else{
"""
cat ${vpairs} > ${sample}.allValidPairs
echo -n "valid_interaction\t" > ${sample}_allValidPairs.mergestat
cat ${vpairs} | wc -l >> ${sample}_allValidPairs.mergestat
echo -n "valid_interaction_rmdup\t" >> ${sample}_allValidPairs.mergestat
cat ${sample}.allValidPairs | wc -l >> ${sample}_allValidPairs.mergestat
## Count short range (<20000) vs long range contacts
awk 'BEGIN{cis=0;trans=0;sr=0;lr=0} \$2 == \$5{cis=cis+1; d=\$6>\$3?\$6-\$3:\$3-\$6; if (d<=20000){sr=sr+1}else{lr=lr+1}} \$2!=\$5{trans=trans+1}END{print "trans_interaction\\t"trans"\\ncis_interaction\\t"cis"\\ncis_shortRange\\t"sr"\\ncis_longRange\\t"lr}' ${sample}.allValidPairs >> ${sample}_allValidPairs.mergestat
## For MultiQC
mkdir -p stats/${sample}
cp ${sample}_allValidPairs.mergestat stats/${sample}/
"""
}
}
process merge_stats {
tag "$ext"
label 'process_low'
publishDir "${params.outdir}/hicpro/", mode: params.publish_dir_mode,
saveAs: {filename -> if (filename.endsWith("stat")) "stats/$filename"}
input:
set val(prefix), file(fstat) from all_mapstat.groupTuple().concat(all_pairstat.groupTuple(), all_rsstat.groupTuple())
output:
file("stats/") into mqc_mstats
file("*stat") into all_mstats
script:
sample = prefix.toString() - ~/(_R1|_R2|_val_1|_val_2|_1|_2)/
if ( (fstat =~ /.mapstat/) ){ ext = "mmapstat" }
if ( (fstat =~ /.pairstat/) ){ ext = "mpairstat" }
if ( (fstat =~ /.RSstat/) ){ ext = "mRSstat" }
"""
merge_statfiles.py -f ${fstat} > ${prefix}.${ext}
mkdir -p stats/${sample}
cp ${prefix}.${ext} stats/${sample}/
"""
}
/*
* HiC-Pro build matrix processes
* kept for backward compatibility
*/
process build_contact_maps{
tag "$sample - $mres"
label 'process_highmem'
publishDir "${params.outdir}/hicpro/matrix/raw", mode: params.publish_dir_mode
when:
!params.skip_maps && params.hicpro_maps
input:
set val(sample), file(vpairs), val(mres) from ch_vpairs.combine(map_res)
file chrsize from chrsize.collect()
output:
set val(sample), val(mres), file("*.matrix"), file("*.bed") into raw_maps, raw_maps_4cool
script:
"""
build_matrix --matrix-format upper --binsize ${mres} --chrsizes ${chrsize} --ifile ${vpairs} --oprefix ${sample}_${mres}
"""
}
process run_ice{
tag "$rmaps"
label 'process_highmem'
publishDir "${params.outdir}/hicpro/matrix/iced", mode: params.publish_dir_mode
when:
!params.skip_maps && !params.skip_balancing && params.hicpro_maps
input:
set val(sample), val(res), file(rmaps), file(bed) from raw_maps
output:
set val(sample), val(res), file("*iced.matrix"), file(bed) into hicpro_iced_maps
file ("*.biases") into hicpro_iced_bias
script:
prefix = rmaps.toString() - ~/(\.matrix)?$/
"""
ice --filter_low_counts_perc ${params.ice_filter_low_count_perc} \
--results_filename ${prefix}_iced.matrix \
--filter_high_counts_perc ${params.ice_filter_high_count_perc} \
--max_iter ${params.ice_max_iter} --eps ${params.ice_eps} --remove-all-zeros-loci --output-bias 1 --verbose 1 ${rmaps}
"""
}
/*
* Cooler
*/
process convert_to_pairs {
tag "$sample"
label 'process_medium'
when:
!params.skip_maps
input:
set val(sample), file(vpairs) from ch_vpairs_cool
file chrsize from chrsize_build.collect()
output:
set val(sample), file("*.txt.gz") into cool_build, cool_build_zoom
script:
"""
## chr/pos/strand/chr/pos/strand
awk '{OFS="\t";print \$1,\$2,\$3,\$5,\$6,\$4,\$7}' $vpairs > contacts.txt
gzip contacts.txt
"""
}
process cooler_raw {
tag "$sample - ${res}"
label 'process_medium'
publishDir "${params.outdir}/contact_maps/", mode: 'copy',
saveAs: {filename -> filename.endsWith(".cool") ? "raw/cool/$filename" : "raw/txt/$filename"}
input:
set val(sample), file(contacts), val(res) from cool_build.combine(map_res_cool)
file chrsize from chrsize_raw.collect()
output:
set val(sample), val(res), file("*cool") into raw_cool_maps
set file("*.bed"), file("${sample}_${res}.txt") into raw_txt_maps
script:
"""
cooler makebins ${chrsize} ${res} > ${sample}_${res}.bed
cooler cload pairs -c1 2 -p1 3 -c2 4 -p2 5 ${sample}_${res}.bed ${contacts} ${sample}_${res}.cool
cooler dump ${sample}_${res}.cool | awk '{OFS="\t"; print \$1+1,\$2+1,\$3}' > ${sample}_${res}.txt
"""
}
process cooler_balance {
tag "$sample - ${res}"
label 'process_medium'
publishDir "${params.outdir}/contact_maps/", mode: 'copy',
saveAs: {filename -> filename.endsWith(".cool") ? "norm/cool/$filename" : "norm/txt/$filename"}
when:
!params.skip_balancing
input:
set val(sample), val(res), file(cool) from raw_cool_maps
file chrsize from chrsize_balance.collect()
output:
set val(sample), val(res), file("${sample}_${res}_norm.cool") into balanced_cool_maps
file("${sample}_${res}_norm.txt") into norm_txt_maps
script:
"""
cp ${cool} ${sample}_${res}_norm.cool
cooler balance ${sample}_${res}_norm.cool -p ${task.cpus} --force
cooler dump ${sample}_${res}_norm.cool --balanced --na-rep 0 | awk '{OFS="\t"; print \$1+1,\$2+1,\$4}' > ${sample}_${res}_norm.txt
"""
}
process cooler_zoomify {
tag "$sample"
label 'process_medium'
publishDir "${params.outdir}/contact_maps/norm/mcool", mode: 'copy'
when:
!params.skip_mcool
input:
set val(sample), file(contacts) from cool_build_zoom
file chrsize from chrsize_zoom.collect()
output:
file("*mcool") into mcool_maps
script:
"""
cooler makebins ${chrsize} ${params.res_zoomify} > bins.bed
cooler cload pairs -c1 2 -p1 3 -c2 4 -p2 5 bins.bed ${contacts} ${sample}.cool
cooler zoomify --nproc ${task.cpus} --balance ${sample}.cool
"""
}
/****************************************************
* DOWNSTREAM ANALYSIS
*/
(maps_cool_insulation, maps_cool_comp, maps_hicexplorer_ddecay, maps_hicexplorer_tads) = balanced_cool_maps.into(4)
/*
* Counts vs distance QC
*/
if (!params.skip_dist_decay){
chddecay = maps_hicexplorer_ddecay.combine(ddecay_res).filter{ it[1] == it[3] }.dump(tag: "ddecay")
}else{
chddecay = Channel.empty()
}
process dist_decay {
tag "$sample"
label 'process_medium'
publishDir "${params.outdir}/dist_decay", mode: 'copy'
when:
!params.skip_dist_decay
input:
set val(sample), val(res), file(maps), val(r) from chddecay
output:
file("*_distcount.txt")
file("*.png")
script:
"""
hicPlotDistVsCounts --matrices ${maps} \
--plotFile ${maps.baseName}_distcount.png \
--outFileData ${maps.baseName}_distcount.txt
"""
}
/*
* Compartment calling
*/
if(!params.skip_compartments){
chcomp = maps_cool_comp.combine(comp_res).filter{ it[1] == it[3] }.dump(tag: "comp")
}else{
chcomp = Channel.empty()
}
process compartment_calling {
tag "$sample - $res"
label 'process_medium'
publishDir "${params.outdir}/compartments", mode: 'copy'
when:
!params.skip_compartments
input:
set val(sample), val(res), file(cool), val(r) from chcomp
file(fasta) from fasta_for_compartments.collect()
file(chrsize) from chrsize_compartments.collect()
output:
file("*compartments*") optional true into out_compartments
script:
"""
cooltools genome binnify --all-names ${chrsize} ${res} > genome_bins.txt
cooltools genome gc genome_bins.txt ${fasta} > genome_gc.txt
cooltools call-compartments --contact-type cis -o ${sample}_compartments ${cool}
awk -F"\t" 'NR>1{OFS="\t"; if(\$6==""){\$6=0}; print \$1,\$2,\$3,\$6}' ${sample}_compartments.cis.vecs.tsv | sort -k1,1 -k2,2n > ${sample}_compartments.cis.E1.bedgraph
"""
}
/*
* TADs calling
*/
if (!params.skip_tads){
chtads = maps_hicexplorer_tads.combine(tads_res_hicexplorer).filter{ it[1] == it[3] }.dump(tag: "hicexp")
}else{
chtads = Channel.empty()
}
process tads_hicexplorer {
tag "$sample - $res"
label 'process_medium'
publishDir "${params.outdir}/tads/hicexplorer", mode: 'copy'
when:
!params.skip_tads && params.tads_caller =~ 'hicexplorer'
input:
set val(sample), val(res), file(cool), val(r) from chtads