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nextflow.config
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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/pcgr Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input/Output options
input = null
outdir = "results"
save_intermediates = false
// Global options for both CPSR & PCGR
genome = null
database = null // this directory must contain code base i.e: pcgr-1.0.3/ and contain data/${params.genome} database file.
save_intermediates = false
// CPSR specific params
panel_id = 0
diagnostic_grade_only = false
ignore_noncoding = false
pop_gnomad = 'nfe'
maf_upper_threshold = 0.9
classify_all = false
clinvar_ignore_noncancer = false
// PCGR params
assay = null
fasta = null
cpsr_report = null // not boolean since 1.1.0. must be path to Gzipped JSON - file ending with 'cpsr.<genome_assembly>.json.gz' - germline report of patient's blood/control sample
tumor_site = 0
tumor_purity = null
tumor_ploidy = null
cna_analysis = false
logr_gain = 0.8
logr_homdel = -0.8
cna_overlap_pct = 50
target_size_mb = 34
estimate_tmb = false
estimate_msi_status = false
tmb_algorithm = 'all_coding'
estimate_signatures = false
min_mutations_signatures = 200
all_reference_signatures = false
include_artefact_signatures = false
prevalence_reference_signatures = 5
include_trials = true
tumor_dp_min = 0
tumor_af_min = 0
control_dp_min = 0
control_af_max = 1
// PCGR tumor only
tumor_only = false
cell_line = false
pon_vcf = null
exclude_pon = false
exclude_likely_hom_germline = false
exclude_likely_het_germline = false
exclude_dbsnp_nonsomatic = false
exclude_nonexonic = false
maf_onekg_eur = 0.002
maf_onekg_amr = 0.002
maf_onekg_afr = 0.002
maf_onekg_eas = 0.002
maf_onekg_sas = 0.002
maf_onekg_global = 0.002
maf_gnomad_nfe = 0.002
maf_gnomad_fin = 0.002
maf_gnomad_asj = 0.002
maf_gnomad_oth = 0.002
maf_gnomad_amr = 0.002
maf_gnomad_afr = 0.002
maf_gnomad_eas = 0.002
maf_gnomad_sas = 0.002
maf_gnomad_global = 0.002
// Variant filtering
filter_haplotypecaller = "-i'FORMAT/DP>10'"
filter_deepvariant = "-i'FORMAT/DP>10'"
filter_strelka_variants = "-i'FORMAT/DP>10'"
filter_freebayes_germline = "-i'FORMAT/DP>10'"
filter_mutect2 = "-i'FORMAT/DP>10'"
filter_freebayes_somatic = "-i'FORMAT/DP>10'"
filter_strelka_indels = "-i'FORMAT/DP>10'"
filter_strelka_snvs = "-i'FORMAT/DP>10'"
// VEP params
vep_n_forks = 4
vep_buffer_size = 500
vep_gencode_all = true
vep_pick_order = 'canonical,appris,biotype,ccds,rank,tsl,length,mane'
vep_no_intergenic = 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 = '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'
genomes = [:]
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_description = null
config_profile_contact = null
config_profile_url = null
config_profile_name = null
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '128.GB'
max_cpus = 16
max_time = '240.h'
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load nf-core/pcgr custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
// try {
// includeConfig "${params.custom_config_base}/pipeline/pcgr.config"
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/pcgr profiles: ${params.custom_config_base}/pipeline/pcgr.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' }
}
// 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 = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "${params.tracedir}/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
}
manifest {
name = 'nf-core/pcgr'
author = 'Barry Digby'
homePage = 'https://github.com/nf-core/pcgr'
description = 'Downstream variant prioritisation using PCGR/CSPR designed to work off nf-core/sarek outputs'
mainScript = 'main.nf'
nextflowVersion = '!>=22.10.4'
version = '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
}
}
}