main.nf 46.75 KiB
#!/usr/bin/env nextflow
/*
========================================================================================
nf-core/hic
========================================================================================
nf-core/hic Analysis Pipeline.
#### Homepage / Documentation
https://github.com/nf-core/hic
----------------------------------------------------------------------------------------
*/
def helpMessage() {
log.info nfcoreHeader()
log.info"""
Usage:
The typical command for running the pipeline is as follows:
nextflow run nf-core/hic --input '*_R{1,2}.fastq.gz' -profile docker
Mandatory arguments:
--input [file] Path to input data (must be surrounded with quotes)
--genome [str] Name of iGenomes reference
-profile [str] Configuration profile to use. Can use multiple (comma separated)
Available: conda, docker, singularity, awsbatch, test and more.
References If not specified in the configuration file or you wish to overwrite any of the references.
--bwt2_index [file] Path to Bowtie2 index
--fasta [file] Path to Fasta reference
Digestion Hi-C If not specified in the configuration file or you wish to set up specific digestion protocol
--digestion [str] Digestion Hi-C. Name of restriction enzyme used for digestion pre-configuration. Default: 'hindiii'
--ligation_site [str] Ligation motifs to trim (comma separated) if not available in --digestion. Default: false
--restriction_site [str] Cutting motif(s) of restriction enzyme(s) (comma separated) if not available in --digestion. Default: false
--chromosome_size [file] Path to chromosome size file
--restriction_fragments [file] Path to restriction fragment file (bed)
--save_reference [bool] Save reference genome to output folder. Default: False
DNase Hi-C
--dnase [bool] Run DNase Hi-C mode. All options related to restriction fragments are not considered. Default: False
--min_cis_dist [int] Minimum intra-chromosomal distance to consider. Default: None
Alignments
--bwt2_opts_end2end [str] Options for bowtie2 end-to-end mappinf (first mapping step). See hic.config for default.
--bwt2_opts_trimmed [str] Options for bowtie2 mapping after ligation site trimming. See hic.config for default.
--min_mapq [int] Minimum mapping quality values to consider. Default: 10
--keep_multi [bool] Keep multi-mapped reads (--min_mapq is ignored). Default: false
--keep_dups [bool] Keep duplicates. Default: false
--save_aligned_intermediates [bool] Save intermediates alignment files. Default: False
--split_fastq [bool] Split fastq files in reads chunks to speed up computation. Default: false
--fastq_chunks_size [int] Size of read chunks if split_fastq is true. Default: 20000000
Valid Pairs Detection
--min_restriction_fragment_size [int] Minimum size of restriction fragments to consider. Default: None
--max_restriction_fragment_size [int] Maximum size of restriction fragments to consider. Default: None
--min_insert_size [int] Minimum insert size of mapped reads to consider. Default: None
--max_insert_size [int] Maximum insert size of mapped reads to consider. Default: None
--save_interaction_bam [bool] Save BAM file with interaction tags (dangling-end, self-circle, etc.). Default: False
Contact maps
--bin_size [str] Bin size for contact maps (comma separated). Default: '1000000,500000'
--ice_max_iter [int] Maximum number of iteration for ICE normalization. Default: 100
--ice_filter_low_count_perc [float] Percentage of low counts columns/rows to filter before ICE normalization. Default: 0.02
--ice_filter_high_count_perc [float] Percentage of high counts columns/rows to filter before ICE normalization. Default: 0
--ice_eps [float] Convergence criteria for ICE normalization. Default: 0.1
Workflow
--skip_maps [bool] Skip generation of contact maps. Useful for capture-C. Default: False
--skip_balancing [bool] Skip contact maps normalization. Default: False --skip_mcool Skip mcool file generation. Default: False
--skip_dist_decay Skip distance decay quality control. Default: False
--skip_tads [bool] Skip TADs calling. Default: False
--skip_multiqc [bool] Skip MultiQC. Default: False
Other options:
--outdir [file] The output directory where the results will be saved
--publish_dir_mode [str] Mode for publishing results in the output directory. Available: symlink, rellink, link, copy, copyNoFollow, move (Default: copy)
--email [email] Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. Default: None
--email_on_fail [email] Same as --email, except only send mail if the workflow is not successful
--max_multiqc_email_size [str] Theshold size for MultiQC report to be attached in notification email. If file generated by pipeline exceeds the threshold, it will not be attached (Default: 25MB)
-name [str] Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic. Default: None
AWSBatch options:
--awsqueue [str] The AWSBatch JobQueue that needs to be set when running on AWSBatch
--awsregion [str] The AWS Region for your AWS Batch job to run on
--awscli [str] Path to the AWS CLI tool
""".stripIndent()
}
/**********************************************************
* SET UP CONFIGURATION VARIABLES
*/
// Show help message
if (params.help){
helpMessage()
exit 0
}
// 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 ${params.digest.keySet().join(", ")}. Please set manually the '--restriction_site' and '--ligation_site' parameters."
}
params.restriction_site = params.digestion ? params.digest[ params.digestion ].restriction_site ?: false : false
params.ligation_site = params.digestion ? params.digest[ params.digestion ].ligation_site ?: false : false
// Check Digestion or DNase Hi-C mode
if (!params.dnase && !params.ligation_site) {
exit 1, "Ligation motif not found. Please either use the `--digestion` parameters or specify the `--restriction_site` and `--ligation_site`. For DNase Hi-C, please use '--dnase' option"
}
// Reference index path configuration
params.bwt2_index = params.genome ? params.genomes[ params.genome ].bowtie2 ?: false : false
params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
// Has the run name been specified by the user?
// this has the bonus effect of catching both -name and --name
custom_runName = params.name
if (!(workflow.runName ==~ /[a-z]+_[a-z]+/)) {
custom_runName = workflow.runName
}
// Check AWS batch settings
if (workflow.profile.contains('awsbatch')) {
// AWSBatch sanity checking
if (!params.awsqueue || !params.awsregion) exit 1, "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
// Check outdir paths to be S3 buckets if running on AWSBatch
// related: https://github.com/nextflow-io/nextflow/issues/813
if (!params.outdir.startsWith('s3:')) exit 1, "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!"
// Prevent trace files to be stored on S3 since S3 does not support rolling files.
if (params.tracedir.startsWith('s3:')) exit 1, "Specify a local tracedir or run without trace! S3 cannot be used for tracefiles."
}
// Stage config filesch_multiqc_config = file("$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 ){
lastPath = params.bwt2_index.lastIndexOf(File.separator)
bwt2_dir = params.bwt2_index.substring(0,lastPath+1)
bwt2_base = params.bwt2_index.substring(lastPath+1)
Channel.fromPath( bwt2_dir , checkIfExists: true)
.ifEmpty { exit 1, "Genome index: Provided index not found: ${params.bwt2_index}" }
.into { bwt2_index_end2end; bwt2_index_trim }
}
else if ( params.fasta ) {
lastPath = params.fasta.lastIndexOf(File.separator)
fasta_base = params.fasta.substring(lastPath+1)
bwt2_base = fasta_base.toString() - ~/(\.fa)?(\.fasta)?(\.fas)?(\.fsa)?$/
Channel.fromPath( params.fasta ) .ifEmpty { exit 1, "Genome index: Fasta file not found: ${params.fasta}" }
.set { 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}
}
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: ${params.fasta}" }
.set { fasta_for_resfrag }
}
else if (! params.dnase) {
exit 1, "No restriction fragments file specified!"
}
if (params.res_tads){
Channel.from( "${params.res_tads}" )
.splitCsv()
.flatten()
.into {tads_res_hicexplorer; tads_res_insulation; tads_bin }
}else{
tads_res=Channel.create()
tads_bin=Channel.create()
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){
Channel.from( "${params.res_dist_decay}" )
.splitCsv()
.flatten()
.into {ddecay_res; ddecay_bin }
}else{
ddecay_res = Channel.create()
ddecay_bin = Channel.create()
if (!params.skip_dist_decay){
log.warn "[nf-core/hic] Hi-C resolution for distance decay not specified. See --res_dist_decay"
}
}
// Resolutions for contact maps
map_res = Channel.from( params.bin_size ).splitCsv().flatten()
map_res.concat(tads_bin, ddecay_bin)
.unique()
.into { map_res; map_res_cool }
/**********************************************************
* SET UP LOGS
*/
// Header log info
log.info nfcoreHeader()
def summary = [:]
if(workflow.revision) summary['Pipeline Release'] = workflow.revision
summary['Run Name'] = custom_runName ?: workflow.runName
summary['Input'] = params.input
summary['splitFastq'] = params.split_fastq
if (params.split_fastq)
summary['Read chunks Size'] = params.fastq_chunks_size
summary['Fasta Ref'] = params.fasta
if (params.restriction_site){
summary['Digestion'] = params.digestion
summary['Restriction Motif']= params.restriction_site
summary['Ligation Motif'] = params.ligation_site
summary['Min Fragment Size']= params.min_restriction_fragment_size
summary['Max Fragment Size']= params.max_restriction_fragment_size
summary['Min Insert Size'] = params.min_insert_size
summary['Max Insert Size'] = params.max_insert_size
}else{
summary['DNase Mode'] = params.dnase
summary['Min CIS dist'] = params.min_cis_dist
}
summary['Min MAPQ'] = params.min_mapq
summary['Keep Duplicates'] = params.keep_dups ? 'Yes' : 'No'
summary['Keep Multihits'] = params.keep_multi ? 'Yes' : 'No'
summary['Maps resolution'] = params.bin_size
summary['Max Resources'] = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job"
if (workflow.containerEngine) summary['Container'] = "$workflow.containerEngine - $workflow.container"
summary['Output dir'] = params.outdir
summary['Launch dir'] = workflow.launchDir
summary['Working dir'] = workflow.workDir
summary['Script dir'] = workflow.projectDir
summary['User'] = workflow.userName
if (workflow.profile.contains('awsbatch')) {
summary['AWS Region'] = params.awsregion
summary['AWS Queue'] = params.awsqueue
summary['AWS CLI'] = params.awscli
}
summary['Config Profile'] = workflow.profile
if (params.config_profile_description) summary['Config Profile Description'] = params.config_profile_description
if (params.config_profile_contact) summary['Config Profile Contact'] = params.config_profile_contact
if (params.config_profile_url) summary['Config Profile URL'] = params.config_profile_url
summary['Config Files'] = workflow.configFiles.join(', ')
if (params.email || params.email_on_fail) {
summary['E-mail Address'] = params.email
summary['E-mail on failure'] = params.email_on_fail
summary['MultiQC maxsize'] = params.max_multiqc_email_size
}
log.info summary.collect { k,v -> "${k.padRight(18)}: $v" }.join("\n")
log.info "-\033[2m--------------------------------------------------\033[0m-"
// Check the hostnames against configured profiles
checkHostname()
Channel.from(summary.collect{ [it.key, it.value] })
.map { k,v -> "<dt>$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 software_versions_yaml
file "software_versions.csv"
script:
"""
echo $workflow.manifest.version > v_pipeline.txt
echo $workflow.nextflow.version > v_nextflow.txt
bowtie2 --version > v_bowtie2.txt
python --version > v_python.txt 2>&1
samtools --version > v_samtools.txt
multiqc --version > v_multiqc.txt
scrape_software_versions.py &> software_versions_mqc.yaml
"""
}
/****************************************************
* PRE-PROCESSING
*/
if(!params.bwt2_index && params.fasta){
process makeBowtie2Index {
tag "$bwt2_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:
"""
mkdir bowtie2_index
bowtie2-build ${fasta} bowtie2_index/${bwt2_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
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 ? "${params.outdir}/mapping" : params.outdir },
saveAs: { params.save_aligned_intermediates ? it : null }, mode: params.publish_dir_mode
input:
set val(sample), file(reads) from raw_reads
file index from bwt2_index_end2end.collect()
output:
set val(sample), file("${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){
"""
bowtie2 --rg-id BMG --rg SM:${prefix} \\
${bwt2_opts} \\
-p ${task.cpus} \\
-x ${index}/${bwt2_base} \\
--un ${prefix}_unmap.fastq \\
-U ${reads} | samtools view -F 4 -bS - > ${prefix}.bam
"""
}else{
"""
bowtie2 --rg-id BMG --rg SM:${prefix} \\
${bwt2_opts} \\
-p ${task.cpus} \\
-x ${index}/${bwt2_base} \\
--un ${prefix}_unmap.fastq \\ -U ${reads} > ${prefix}.bam
"""
}
}
process trim_reads {
tag "$sample"
label 'process_low'
publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping" : params.outdir },
saveAs: { params.save_aligned_intermediates ? it : null }, mode: params.publish_dir_mode
when:
!params.dnase
input:
set val(sample), file(reads) from unmapped_end_to_end
output:
set val(sample), file("${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 ? "${params.outdir}/mapping" : params.outdir },
saveAs: { params.save_aligned_intermediates ? it : null }, mode: params.publish_dir_mode
when:
!params.dnase
input:
set val(sample), file(reads) from trimmed_reads
file index from bwt2_index_trim.collect()
output:
set val(sample), file("${prefix}_trimmed.bam") into trimmed_bam
script:
prefix = reads.toString() - ~/(_trimmed)?(\.fq)?(\.fastq)?(\.gz)?$/
"""
bowtie2 --rg-id BMG --rg SM:${prefix} \\
${params.bwt2_opts_trimmed} \\
-p ${task.cpus} \\
-x ${index}/${bwt2_base} \\
-U ${reads} | samtools view -bS - > ${prefix}_trimmed.bam
"""
}
if (!params.dnase){
process bowtie2_merge_mapping_steps{
tag "$prefix = $bam1 + $bam2"
label 'process_medium'
publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping" : params.outdir },
saveAs: { params.save_aligned_intermediates ? it : null }, mode: params.publish_dir_mode
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|_val_1|_val_2|_1|_2)/
sample = prefix.toString() - ~/(_R1|_R2)/
//tag = prefix.toString() =~/_R1|_val_1|_1/ ? "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 -T /tmp/ \\
-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 = $bam"
label 'process_medium'
publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping" : params.outdir },
saveAs: { params.save_aligned_intermediates ? it : null }, mode: params.publish_dir_mode
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("${prefix}.mapstat") into all_mapstat
script:
//sample = prefix.toString() - ~/(_R1|_R2|_val_1|_val_2|_1|_2)/
sample = prefix.toString() - ~/(_R1|_R2)/
//tag = prefix.toString() =~/_R1|_val_1|_1/ ? "R1" : "R2"
tag = prefix.toString() =~/_R1/ ? "R1" : "R2"
oname = prefix.toString() - ~/(\.[0-9]+)$/
"""
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}/mapping", mode: params.publish_dir_mode,
saveAs: {filename -> filename.indexOf(".pairstat") > 0 ? "stats/$filename" : "$filename"}
input:
set val(sample), file(aligned_bam) from bwt2_merged_bam.groupTuple().dump(tag:'mates')
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 "${params.outdir}/valid_pairs", mode: params.publish_dir_mode,
saveAs: {filename -> filename.indexOf(".stat") > 0 ? "stats/$filename" : "$filename"}
input:
set val(sample), file(pe_bam) from paired_bam
file frag_file from res_frag_file.collect()
output:
set val(sample), file("*.validPairs") into valid_pairs
set val(sample), file("*.validPairs") into valid_pairs_4cool
set val(sample), file("*.DEPairs") into de_pairs
set val(sample), file("*.SCPairs") into sc_pairs
set val(sample), file("*.REPairs") into re_pairs
set val(sample), file("*.FiltPairs") into filt_pairs
set val(sample), file("*RSstat") into all_rsstat
script:
if (params.split_fastq){
sample = sample.toString() - ~/(\.[0-9]+)$/
}
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 -T /tmp/ -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 "${params.outdir}/valid_pairs", mode: params.publish_dir_mode,
saveAs: {filename -> filename.indexOf(".stat") > 0 ? "stats/$filename" : "$filename"}
input:
set val(sample), file(pe_bam) from paired_bam
output:
set val(sample), file("*.validPairs") into valid_pairs
set val(sample), file("*.validPairs") into valid_pairs_4cool
set val(sample), file("*RSstat") into all_rsstat
script:
if (params.split_fastq){
sample = sample.toString() - ~/(\.[0-9]+)$/
}
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 -T /tmp/ -k2,2V -k3,3n -k5,5V -k6,6n -o ${prefix}.validPairs ${prefix}.validPairs
"""
}
}
/*
* Remove duplicates
*/
process remove_duplicates {
tag "$sample"
label 'process_highmem'
publishDir "${params.outdir}/valid_pairs", mode: params.publish_dir_mode,
saveAs: {filename -> filename.indexOf(".stat") > 0 ? "stats/$sample/$filename" : "$filename"}
input:
set val(sample), file(vpairs) from valid_pairs.groupTuple().dump(tag:'final')
output:
set val(sample), file("*.allValidPairs") into ch_vpairs, ch_vpairs_cool
file("stats/") 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 -T /tmp/ -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}' > ${sample}.allValidPairs
echo -n "valid_interaction\t" > stats/${sample}/${sample}_allValidPairs.mergestat
cat ${vpairs} | wc -l >> stats/${sample}/${sample}_allValidPairs.mergestat
echo -n "valid_interaction_rmdup\t" >> stats/${sample}/${sample}_allValidPairs.mergestat
cat ${sample}.allValidPairs | wc -l >> stats/${sample}/${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}' ${sample}.allValidPairs >> stats/${sample}/${sample}_allValidPairs.mergestat
"""
}else{
"""
mkdir -p stats/${sample}
cat ${vpairs} > ${sample}.allValidPairs
echo -n "valid_interaction\t" > stats/${sample}/${sample}_allValidPairs.mergestat
cat ${vpairs} | wc -l >> stats/${sample}/${sample}_allValidPairs.mergestat
echo -n "valid_interaction_rmdup\t" >> stats/${sample}/${sample}_allValidPairs.mergestat
cat ${sample}.allValidPairs | wc -l >> stats/${sample}/${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}' ${sample}.allValidPairs >> stats/${sample}/${sample}_allValidPairs.mergestat
"""
}
}
process merge_stats {
tag "$ext"
label 'process_low'
publishDir "${params.outdir}/stats/${sample}", mode: params.publish_dir_mode
input:
set val(prefix), file(fstat) from all_mapstat.groupTuple().concat(all_pairstat.groupTuple(), all_rsstat.groupTuple())
output:
file("mstats/") 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" }
"""
mkdir -p mstats/${sample}
merge_statfiles.py -f ${fstat} > mstats/${sample}/${prefix}.${ext}
"""
}
/*
* HiC-Pro build matrix processes
* ONGOING VALIDATION - TO REPLACED BY COOLER ?
*/
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
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_ice
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 iced_maps_4h5, iced_maps_4cool
file ("*.biases") into iced_bias
script: prefix = rmaps.toString() - ~/(\.matrix)?$/
"""
ice --filter_low_counts_perc ${params.ice_filer_low_count_perc} \
--results_filename ${prefix}_iced.matrix \
--filter_high_counts_perc ${params.ice_filer_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.indexOf(".cool") > 0 ? "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.indexOf(".cool") > 0 ? "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 norm_cool_maps, norm_cool_maps_h5
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 ${sample}.cool
"""
}
/*
* Create h5 file
*/
process convert_to_h5 {
tag "$sample"
label 'process_medium'
publishDir "${params.outdir}/contact_maps/norm/h5", mode: 'copy'
input:
set val(sample), val(res), file(maps) from norm_cool_maps_h5
output:
set val(sample), val(res), file("*.h5") into h5maps_ddecay, h5maps_ccomp, h5maps_tads
script:
"""
hicConvertFormat --matrices ${maps} \
--outFileName ${maps.baseName}.h5 \
--resolution ${res} \
--inputFormat cool \
--outputFormat h5 \
"""
}
/****************************************************
* DOWNSTREAM ANALYSIS
*/
/*
* Counts vs distance QC
*/
chddecay = h5maps_ddecay.combine(ddecay_res).filter{ it[1] == it[3] }.dump(tag: "ddecay")
process dist_decay {
tag "$sample"
label 'process_medium'
publishDir "${params.outdir}/dist_decay", mode: 'copy'
when:
!params.skip_dist_decay
input:
set val(sample), val(res), file(h5mat), val(r) from chddecay
output:
file("*_distcount.txt")
file("*.png")
script:
"""
hicPlotDistVsCounts --matrices ${h5mat} \
--plotFile ${h5mat.baseName}_distcount.png \
--outFileData ${h5mat.baseName}_distcount.txt
"""
}
/*
* Compartment calling
*/
/*
chcomp = iced_maps_comp.combine(comp_res).filter{ it[1] == it[4] }.dump(tag: "comp")
process compartment_calling {
tag "$sample - $res"
label 'process_medium'
publishDir "${params.outdir}/compartments", mode: 'copy'
when:
!params.skip_compartments
input:
set val(sample), val(res), file(mat), file(bed), val(r) from chcomp
output:
file("*.bedgraph") optional true into out_compartments
script:
"""
call_compartments.r --matrix ${mat} --bed ${bed}
"""
}
*/
/*
* TADs calling
*/
chtads = h5maps_tads.combine(tads_res_hicexplorer).filter{ it[1] == it[3] }.dump(tag: "hicexp")
process tads_hicexplorer {
tag "$sample - $res"
label 'process_medium'
publishDir "${params.outdir}/tads", mode: 'copy'
when:
!params.skip_tads && params.tads_caller =~ 'hicexplorer'
input:
set val(sample), val(res), file(h5mat), val(r) from chtads
output:
file("*.{bed,bedgraph,gff}") into hicexplorer_tads
script:
"""
hicFindTADs --matrix ${h5mat} \
--outPrefix tad \
--correctForMultipleTesting fdr \
--numberOfProcessors ${task.cpus}
"""
}
chIS = norm_cool_maps.combine(tads_res_insulation).filter{ it[1] == it[3] }.dump(tag : "ins")
process tads_insulation {
tag "$sample - $res"
label 'process_medium'
publishDir "${params.outdir}/tads", mode: 'copy'
when:
!params.skip_tads && params.tads_caller =~ 'insulation'
input:
set val(sample), val(res), file(cool), val(r) from chIS
output:
file("*tsv") into insulation_tads
script:
"""
cooltools diamond-insulation --window-pixels ${cool} 15 25 50 > ${sample}_insulation.tsv
"""
}
/*
* MultiQC
*/
process multiqc {
label 'process_low'
publishDir "${params.outdir}/MultiQC", mode: params.publish_dir_mode
when:
!params.skip_multiqc
input:
file multiqc_config from ch_multiqc_config
file (mqc_custom_config) from ch_multiqc_custom_config.collect().ifEmpty([])
file ('input_*/*') from all_mstats.concat(all_mergestat).collect()
file ('software_versions/*') from software_versions_yaml
file workflow_summary from ch_workflow_summary.collect()
output:
file "*multiqc_report.html" into multiqc_report
file "*_data"
script:
rtitle = custom_runName ? "--title \"$custom_runName\"" : ''
rfilename = custom_runName ? "--filename " + custom_runName.replaceAll('\\W','_').replaceAll('_+','_') + "_multiqc_report" : ''
"""
multiqc -f $rtitle $rfilename --config $multiqc_config .
"""
}
/*
* Output Description HTML
*/
process output_documentation {
publishDir "${params.outdir}/pipeline_info", mode: params.publish_dir_mode
input:
file output_docs from ch_output_docs
file images from ch_output_docs_images
output:
file "results_description.html"
script:
"""
markdown_to_html.py $output_docs -o results_description.html
"""
}
/*
* Completion e-mail notification
*/
workflow.onComplete {
// Set up the e-mail variables
def subject = "[nf-core/hic] Successful: $workflow.runName"
if (!workflow.success) {
subject = "[nf-core/hic] FAILED: $workflow.runName"
}
def email_fields = [:]
email_fields['version'] = workflow.manifest.version
email_fields['runName'] = custom_runName ?: workflow.runName
email_fields['success'] = workflow.success
email_fields['dateComplete'] = workflow.complete
email_fields['duration'] = workflow.duration
email_fields['exitStatus'] = workflow.exitStatus
email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
email_fields['errorReport'] = (workflow.errorReport ?: 'None')
email_fields['commandLine'] = workflow.commandLine
email_fields['projectDir'] = workflow.projectDir
email_fields['summary'] = summary
email_fields['summary']['Date Started'] = workflow.start
email_fields['summary']['Date Completed'] = workflow.complete
email_fields['summary']['Pipeline script file path'] = workflow.scriptFile
email_fields['summary']['Pipeline script hash ID'] = workflow.scriptId
if (workflow.repository) email_fields['summary']['Pipeline repository Git URL'] = workflow.repository
if (workflow.commitId) email_fields['summary']['Pipeline repository Git Commit'] = workflow.commitId
if (workflow.revision) email_fields['summary']['Pipeline Git branch/tag'] = workflow.revision
email_fields['summary']['Nextflow Version'] = workflow.nextflow.version
email_fields['summary']['Nextflow Build'] = workflow.nextflow.build
email_fields['summary']['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
// On success try attach the multiqc report
def mqc_report = null
try {
if (workflow.success) {
mqc_report = ch_multiqc_report.getVal()
if (mqc_report.getClass() == ArrayList) {
log.warn "[nf-core/hic] Found multiple reports from process 'multiqc', will use only one"
mqc_report = mqc_report[0]
}
}
} catch (all) {
log.warn "[nf-core/hic] Could not attach MultiQC report to summary email"
}
// Check if we are only sending emails on failure email_address = params.email
if (!params.email && params.email_on_fail && !workflow.success) {
email_address = params.email_on_fail
}
// Render the TXT template
def engine = new groovy.text.GStringTemplateEngine()
def tf = new File("$projectDir/assets/email_template.txt")
def txt_template = engine.createTemplate(tf).make(email_fields)
def email_txt = txt_template.toString()
// Render the HTML template
def hf = new File("$projectDir/assets/email_template.html")
def html_template = engine.createTemplate(hf).make(email_fields)
def email_html = html_template.toString()
// Render the sendmail template
def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: params.max_multiqc_email_size.toBytes() ]
def sf = new File("$projectDir/assets/sendmail_template.txt")
def sendmail_template = engine.createTemplate(sf).make(smail_fields)
def sendmail_html = sendmail_template.toString()
// Send the HTML e-mail
if (email_address) {
try {
if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
// Try to send HTML e-mail using sendmail
[ 'sendmail', '-t' ].execute() << sendmail_html
log.info "[nf-core/hic] Sent summary e-mail to $email_address (sendmail)"
} catch (all) {
// Catch failures and try with plaintext
def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
if ( mqc_report.size() <= params.max_multiqc_email_size.toBytes() ) {
mail_cmd += [ '-A', mqc_report ]
}
mail_cmd.execute() << email_html
log.info "[nf-core/hic] Sent summary e-mail to $email_address (mail)"
}
}
// Write summary e-mail HTML to a file
def output_d = new File("${params.outdir}/pipeline_info/")
if (!output_d.exists()) {
output_d.mkdirs()
}
def output_hf = new File(output_d, "pipeline_report.html")
output_hf.withWriter { w -> w << email_html }
def output_tf = new File(output_d, "pipeline_report.txt")
output_tf.withWriter { w -> w << email_txt }
c_green = params.monochrome_logs ? '' : "\033[0;32m";
c_purple = params.monochrome_logs ? '' : "\033[0;35m";
c_red = params.monochrome_logs ? '' : "\033[0;31m";
c_reset = params.monochrome_logs ? '' : "\033[0m";
if (workflow.stats.ignoredCount > 0 && workflow.success) {
log.info "-${c_purple}Warning, pipeline completed, but with errored process(es) ${c_reset}-"
log.info "-${c_red}Number of ignored errored process(es) : ${workflow.stats.ignoredCount} ${c_reset}-"
log.info "-${c_green}Number of successfully ran process(es) : ${workflow.stats.succeedCount} ${c_reset}-"
}
if (workflow.success) {
log.info "-${c_purple}[nf-core/hic]${c_green} Pipeline completed successfully${c_reset}-"
} else {
checkHostname()
log.info "-${c_purple}[nf-core/hic]${c_red} Pipeline completed with errors${c_reset}-"
}
}
def nfcoreHeader() {
// Log colors ANSI codes
c_black = params.monochrome_logs ? '' : "\033[0;30m";
c_blue = params.monochrome_logs ? '' : "\033[0;34m";
c_cyan = params.monochrome_logs ? '' : "\033[0;36m";
c_dim = params.monochrome_logs ? '' : "\033[2m";
c_green = params.monochrome_logs ? '' : "\033[0;32m";
c_purple = params.monochrome_logs ? '' : "\033[0;35m";
c_reset = params.monochrome_logs ? '' : "\033[0m";
c_white = params.monochrome_logs ? '' : "\033[0;37m";
c_yellow = params.monochrome_logs ? '' : "\033[0;33m";
return """ -${c_dim}--------------------------------------------------${c_reset}-
${c_green},--.${c_black}/${c_green},-.${c_reset}
${c_blue} ___ __ __ __ ___ ${c_green}/,-._.--~\'${c_reset}
${c_blue} |\\ | |__ __ / ` / \\ |__) |__ ${c_yellow}} {${c_reset}
${c_blue} | \\| | \\__, \\__/ | \\ |___ ${c_green}\\`-._,-`-,${c_reset}
${c_green}`._,._,\'${c_reset}
${c_purple} nf-core/hic v${workflow.manifest.version}${c_reset}
-${c_dim}--------------------------------------------------${c_reset}-
""".stripIndent()
}
def checkHostname() {
def c_reset = params.monochrome_logs ? '' : "\033[0m"
def c_white = params.monochrome_logs ? '' : "\033[0;37m"
def c_red = params.monochrome_logs ? '' : "\033[1;91m"
def c_yellow_bold = params.monochrome_logs ? '' : "\033[1;93m"
if (params.hostnames) {
def hostname = "hostname".execute().text.trim()
params.hostnames.each { prof, hnames ->
hnames.each { hname ->
if (hostname.contains(hname) && !workflow.profile.contains(prof)) {
log.error "====================================================\n" +
" ${c_red}WARNING!${c_reset} You are running with `-profile $workflow.profile`\n" +
" but your machine hostname is ${c_white}'$hostname'${c_reset}\n" +
" ${c_yellow_bold}It's highly recommended that you use `-profile $prof${c_reset}`\n" +
"============================================================"
}
}
}
}
}