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nextflow.config
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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samurai Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
// References
genome = "hg38"
igenomes_base = 's3://ngi-igenomes/igenomes'
igenomes_ignore = false
// Alignment options
index_genome = false
aligner = null
aligner_index = null
// Trimming options
run_fastp = false
fastp_umi_loc = null
fastp_umi_length = null
fastp_umi_skip = null
fastp_min_read_length = null
fastp_cut_window_size = 4
fastp_min_quality = null
fastp_max_trimmed_pct = null
fastp_trim_poly_x = false
fastp_trim_poly_g = false
// Size selection options
size_selection = false
title = "Fragment size distribution"
max_fragmentsize = 400
// Segmentation / CNV calling options
binsize = 500
purity = 1
// CN Calling algorithms
caller = 'qdnaseq'
analysis_type = 'solid_biopsy'
// Liquid Biopsy Options
normal_panel = null
pon_path = null
pon_name = "PoN"
build_pon = false
selection_maxsize = 150
filter_bam_pon = false // TO DO: FIX this
plot_fragment_distribution = false
// QDNAseq
qdnaseq_bin_data = null
qdnaseq_paired_ends = true
// ichorCNA
ichorcna_genome_style = 'UCSC'
ichorcna_readcounter_chrs = "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22"
ichorcna_readcounter_quality = 20
ichorcna_chrs_to_use = "paste0('chr', c(1:22))"
ichorcna_chrs_to_train = "paste0('chr', c(1:22))"
ichorcna_chrs_to_normalize = "paste0('chr', c(1:22))"
ichorcna_estimate_normal = "TRUE"
ichorcna_fraction_reads_male = 0.001
ichorcna_male_chrX_logR = 0.3
ichorcna_min_map_score = 0.75
ichorcna_max_frac_genome_subclone = 0.5
ichorcna_max_frac_cna_subclone = 0.7
ichorcna_min_segment_bins = 50
ichorcna_max_cn = 5
ichorcna_include_homd = "FALSE"
ichorcna_txne = 0.9999
ichorcna_alt_frac_threshold = 0.05
ichorcna_trx_strength = 10000
ichorcna_plotfiletype = "pdf"
ichorcna_plotylim = "c(-2,4)"
ichorcna_estimate_sc = false
ichorcna_estimate_ploidy = true
ichorcna_filter_bam_pon = false
ichorcna_normal_states = "0.5, 0.6, 0.7, 0.8, 0.9, 0.95, 0.99"
ichorcna_gc_wig = null
ichorcna_map_wig = null
ichorcna_reptime_wig = null
// FIXME: Supply it with the pipeline
ichorcna_centromere_file = null
// WisecondorX
wisecondorx_no_rm_dup = false
wisecondorx_yfrac = 0.4
wisecondorx_ylim = null
wisecondorx_zscore = 5
wisecondorx_blacklist = null
// ASCAT.sc
ascat_sc_predict_refit = "TRUE"
ascat_sc_segmentation_alpha = 0.01
ascat_sc_min_purity = 0.01
ascat_sc_max_purity = 1
ascat_sc_min_ploidy = 1.7
ascat_sc_max_ploidy = 5
ascat_sc_max_tumor_ploidy = 5
// Signatures
compute_signatures = false
// Gistic2
run_gistic = false
gistic_t_amp = 0.1
gistic_t_del = 0.1
gistic_remove_x = false
gistic_conf = 0.99
gistic_qval = 0.05
gistic_broad_analysis = false
gistic_broad_chr_length = 0.99
gistic_cn_cap = 6
// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = "${projectDir}/assets/dincalcilab-samurai_logo_dark.png"
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null
// Boilerplate options
outdir = null
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
version = false
validate_params = true
show_hidden_params = false
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${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'
// Schema validation default options
validationSchemaIgnoreParams = 'genomes,igenomes_base,fasta,fai,dict'
validationShowHiddenParams = false
validate_params = true
}
// 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: ${params.custom_config_base}/nfcore_custom.config")
}
// Load dincalcilab/samurai custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
// try {
// includeConfig "${params.custom_config_base}/pipeline/samurai.config"
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/samurai profiles: ${params.custom_config_base}/pipeline/samurai.config")
// }
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.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' }
}
// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry = 'quay.io'
docker.registry = 'quay.io'
podman.registry = 'quay.io'
singularity.registry = 'quay.io'
// 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}.html"
}
// Nextflow plugins
plugins {
id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
manifest {
name = 'dincalcilab/samurai'
author = 'Sara Potente, Luca Beltrame'
homePage = 'https://github.com/dincalcilab/samurai'
description = "SAMURAI: Shallow Analysis of Copy nuMber alterations Using a Reproducible And Integrated bioinformatics pipeline"
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
version = '1.0.3'
doi = '10.1101/2024.09.30.615766'
}
// 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
}
}
}