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nextflow.config
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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/hicar Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
method = 'HiCAR'
anchor_peaks = null
// References
genome = null
igenomes_base = 's3://ngi-igenomes/igenomes'
igenomes_ignore = false
ucscname = null
mappability = null
blacklist = null
//trim reads
skip_cutadapt = false
// Enzyme
enzyme = 'CviQI'
restriction_sites = '^TAC'
restriction_sites_cut_off = 0.5
// ATAC peak calling
shiftsize = -75
smooth_window = 150
qval_thresh = 0.01
// R1 peak calling
high_resolution_R1 = false
r1_pval_thresh = 0.1
// HiPeak calling
remove_dup = false
snow_type = "SOCK"
peak_pair_block = 1e8
// Options: Peaks
skip_peak_qc = false
skip_peak_annotation = false
// Options: Differential analysis
skip_diff_analysis = false
enrichment_fdr = 0.05
// MAPS bins, MAPS resolution
cool_bin = '5000_10000'
maps_digest_file = null
maps_cutoff_counts = 12
maps_cutoff_fold_change = 2
maps_cutoff_fdr = 2
maps_filter = 'None'
maps_model = 'pospoisson'
merge_map_py_source = 'https://raw.githubusercontent.com/ijuric/MAPS/91c9c360092b25a217d91b9ea07eba5dd2ac72f4/bin/utils/genomic_features_generator/scripts/merge_map.py'
feature_frag2bin_source = 'https://raw.githubusercontent.com/ijuric/MAPS/91c9c360092b25a217d91b9ea07eba5dd2ac72f4/bin/utils/genomic_features_generator/scripts/feature_frag2bin.py'
make_maps_runfile_source = 'https://raw.githubusercontent.com/ijuric/MAPS/18c1a337f222130d7c5735d051614e2a253d5319/bin/MAPS/make_maps_runfile.py'
// Options: QC
skip_fastqc = false
skip_plot_profile = false
skip_igv = false
skip_multiqc = false
skip_trackhub = false
skip_enrichment = true
// Options: v4c
virtual_4c = false
v4c_max_events = 25
// MultiQC options
multiqc_config = null
multiqc_title = null
max_multiqc_email_size = '25.MB'
// Boilerplate options
outdir = null
tracedir = "${params.outdir}/pipeline_info"
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
help = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes'
enable_conda = false
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${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 = '156.GB'
max_cpus = 16
max_time = '240.h'
// Juicer Java paramaters
juicer_jvm_params = '-Xms512m -Xmx4096m'
juicer_tools_jar = 'https://github.com/aidenlab/Juicebox/releases/download/v2.13.06/juicer_tools_2.13.06.jar'
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load nf-core/hicar custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
// try {
// includeConfig "${params.custom_config_base}/pipeline/hicar.config"
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/hicar profiles: ${params.custom_config_base}/pipeline/hicar.config")
// }
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' }
test_hipeak { includeConfig 'conf/test_hipeak.config' }
test_multi { includeConfig 'conf/test_multi.config' }
test_hichip { includeConfig 'conf/test_hichip.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.
env {
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']
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.svg"
}
manifest {
name = 'nf-core/hicar'
author = 'Jianhong Ou, Yu Xiang, Yarui Diao'
homePage = 'https://github.com/nf-core/hicar'
description = 'This pipeline analyses data for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.'
mainScript = 'main.nf'
nextflowVersion = '!>=21.10.3'
version = '1.1.0dev'
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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
}
}
}