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========================================================================================
nf-core/hic Nextflow config file
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Default config options for all compute environments
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*/
// Global default params, used in configs
params {
// TODO nf-core: Specify your pipeline's command line flags
// Input options
input = null
// References
genome = null
igenomes_base = 's3://ngi-igenomes/igenomes'
igenomes_ignore = false
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chromosome_size = false
restriction_fragments = false
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 = false
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^ANT'
ligation_site='GATCGATC,GATCGANT,GANTGATC,GANTGANT'
}
}
min_restriction_fragment_size = 0
max_restriction_fragment_size = 0
min_insert_size = 0
max_insert_size = 0
save_nonvalid_pairs = false
// Dnase Hi-C
dnase = false
min_cis_dist = 0
// Contact maps
bin_size = '1000000'
res_zoomify = '5000'
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
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// MultiQC options
multiqc_config = null
multiqc_title = null
max_multiqc_email_size = '25.MB'
// Boilerplate options
outdir = './results'
tracedir = "${params.outdir}/pipeline_info"
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
help = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes,modules'
enable_conda = false
singularity_pull_docker_container = false
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
hostnames = [:]
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'
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// Load nf-core custom profiles from different Institutions
includeConfig "${params.custom_config_base}/nfcore_custom.config"
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load igenomes.config if required
if (!params.igenomes_ignore) {
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includeConfig 'conf/igenomes.config'
} else {
params.genomes = [:]
}
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
conda {
params.enable_conda = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
docker {
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
shifter.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
enabled = true
file = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
enabled = true
file = "${params.tracedir}/execution_report_${trace_timestamp}.html"
enabled = true
file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
enabled = true
file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.svg"
name = 'nf-core/hic'
author = 'Nicolas Servant'
homePage = 'https://github.com/nf-core/hic'
description = 'Analysis of Chromosome Conformation Capture data (Hi-C)'
mainScript = 'main.nf'
nextflowVersion = '!>=21.04.0'
version = '1.3.0'
}
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
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if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'time') {
try {
if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
return params.max_time as nextflow.util.Duration
else
return obj
} catch (all) {
println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'cpus') {
try {
return Math.min( obj, params.max_cpus as int )
} catch (all) {
println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
return obj
}