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nextflow.config
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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dincalcilab/lowfrac-variant-benchmark Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input_all = null
input_normal = null
input_tumor = null
// References
// genome = 'hg38'
// MultiQC options
multiqc_config = null
multiqc_title = null
max_multiqc_email_size = '25.MB'
// Boilerplate options
outdir = null
tracedir = "${params.outdir}/pipeline_info"
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
help = false
validate_params = false
show_hidden_params = false
schema_ignore_params = 'genomes'
enable_conda = false
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${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 = '128.GB'
max_cpus = 60
max_time = '240.h'
// Workflow options
fasta = null
fasta_fai = null
bed = null
samples = 2
skip_normal_generation = null
skip_tumor_generation = null
skip_variant_calling = null
tumor_only = null
paired_mode = null
pon_mode = null
high_sensitivity = null
//NEAT options
neat_path = null
readlen = 151
coverage = 100
error_model = "$HOME/.nextflow/assets/DIncalciLab/LFV-benchmark/assets/neat_models/errorModel_default.pickle.gz"
mutation_model = "$HOME/.nextflow/assets/DIncalciLab/LFV-benchmark/assets/neat_models/MutModel_NA12878.pickle.gz"
gc_model = "$HOME/.nextflow/assets/DIncalciLab/LFV-benchmark/assets/neat_models/gcBias_default.pickle.gz"
fraglen_model = "$HOME/.nextflow/assets/DIncalciLab/LFV-benchmark/assets/neat_models/fraglenModel_default.pickle.gz"
//BAMSurgeon options
spikein = 'random'
mut_number = 100
maxlen = 30
min_fraction = 0.0001
max_fraction = 0.05
type = 'both'
picardjar = "$HOME/.nextflow/assets/DIncalciLab/LFV-benchmark/assets/picard.jar"
///Variant calling options
//General options
skip_vardict = null
skip_mutect = null
skip_varscan = null
skip_lofreq = null
skip_strelka = null
skip_freebayes = null
//Mutect options
germline_resource = null
panel_of_normals = null
dbsnp_vcf = null
//Strelka2 options
manta_candidate_small_indels = null
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
conda {
params.enable_conda = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
docker {
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
shifter.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
}
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
JULIA_DEPOT_PATH = "/usr/local/share/julia"
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${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_${trace_timestamp}.html"
}
manifest {
name = 'dincalcilab/LFV-benchmark'
author = 'Aldo Sergi, Luca Beltrame'
homePage = 'https://github.com/dincalcilab/lowfrac-variant-benchmark'
description = 'Workflow to generate syntethic data sets with artificial low fraction variants to benchmark somatic variant callers'
mainScript = 'main.nf'
nextflowVersion = '!>=21.10.3'
version = '1.0dev'
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// Load configuration for local testing
includeConfig 'conf/test_local.config'
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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
}
}
}