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'