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Default config options for all compute environments
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*/
// Global default params, used in configs
params {
// Choice of the workflow ('hicpro' or 'hicstuff')
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'
//Save bam filtered by Picard
save_bam_intermediates = 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^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
// Dnase Hi-C
dnase = false
min_cis_dist = 0
// Contact maps
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_methods_description = null
// Boilerplate options
outdir = './results'
tracedir = "${params.outdir}/pipeline_info"
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes,digest,bin_size,res_dist_decay,res_tads,res_compartments'
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${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
// 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_matrix = 'abs_fragments_contacts_weighted.txt'
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' //string number (ex: '30') or 'None'
hicstuff_distance_plot = 'false'
hicstuff_distance_out_plot = 'plot_distance_law.pdf'
hicstuff_filter_pcr_out_file = 'valid_idx_pcrfree.pairs'
hicstuff_read_len = 'None'
hicstuff_tmp_dir = 'None'
//Hicstuff optional modules
filter_event = false
distance_law = false
filter_pcr = false
//Hicstuff save intermediates files
save_fragments = false
//Parasplit
parasplit_mode = 'all'
parasplit_seed = 20
//Iterative alignement
iteralign = false
}
// 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: ${params.custom_config_base}/nfcore_custom.config")
// Load nf-core/hic custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
// try {
// includeConfig "${params.custom_config_base}/pipeline/hic.config"
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/hic profiles: ${params.custom_config_base}/pipeline/hic.config")
// }
debug {
dumpHashes = true
process.beforeScript = 'echo $HOSTNAME'
cleanup = false
}
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.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.registry = 'quay.io'
conda.enabled = false
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
apptainer.enabled = false
}
apptainer {
apptainer.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
gitpod {
executor.name = 'local'
executor.cpus = 16
executor.memory = 60.GB
}
public_aws_ecr {
includeConfig 'conf/public_aws_ecr.config'
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
// Load igenomes.config if required
if (!params.igenomes_ignore) {
includeConfig 'conf/igenomes.config'
} else {
params.genomes = [:]
}
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
JULIA_DEPOT_PATH = "/usr/local/share/julia"
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
// Set default registry for Docker and Podman independent of -profile
// Will not be used unless Docker / Podman are enabled
// Set to your registry if you have a mirror of containers
docker.registry = 'quay.io'
podman.registry = 'quay.io'
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"
fields = "task_id,hash,name,status,exit,duration,submit,realtime,%cpu,%mem,peak_rss,peak_vmem,rchar,wchar"
file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
author = """Nicolas Servant"""
description = """Analysis of Chromosome Conformation Capture data (Hi-C)"""
nextflowVersion = '!>=22.10.1'
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// 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
}