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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ferlab/postprocessing Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// TODO nf-core: Specify your pipeline's command line flags
// Input options
input = null
// References
genome = null
igenomes_base = 's3://ngi-igenomes/igenomes/'
igenomes_ignore = false
referenceGenome = null
referenceGenomeFasta = null
broad = null
intervalsFile = null
dbsnpFile = null
dbsnpFileIndex = null
tools = ""
vep_cache = null
vep_cache_version = null
vep_genome = null
exomiser_genome = null
exomiser_data_dir = null
exomiser_data_version = null
exomiser_cadd_version = null
exomiser_cadd_indel_filename = null
exomiser_cadd_snv_filename = null
exomiser_remm_version = null
exomiser_remm_filename = null
exomiser_analysis_wes = "${projectDir}/assets/exomiser/default_exomiser_WES_analysis.yml"
exomiser_analysis_wgs = "${projectDir}/assets/exomiser/default_exomiser_WGS_analysis.yml"
exomiser_local_frequency_path = null
exomiser_local_frequency_index_path = null
exomiser_start_from_vep = false
//Process-specific parameters
exclude_mnps = true
TSfilterSNP = '99'
TSfilterINDEL = '99'
hardFilters = [[name: 'QD2', expression: 'QD < 2.0'],
[name: 'QD1', expression: 'QD < 1.0'],
[name: 'QUAL30', expression: 'QUAL < 30.0'],
[name: 'SOR3', expression: 'SOR > 3.0'],
[name: 'FS60', expression: 'FS > 60.0'],
[name: 'MQ40', expression: 'MQ < 40.0'],
[name: 'MQRankSum-12.5', expression: 'MQRankSum < -12.5'],
[name: 'ReadPosRankSum-8', expression: 'ReadPosRankSum < -8.0']]
allow_old_gatk_data = false
//Resources optionsreferenceGenome
//defaults expecting to be overwritten
max_cpus = 16
max_disk = '200.GB'
max_time = '12.h'
max_memory = '120.GB'
// Boilerplate options
outdir = null
publish_all = false
publish_dir_mode = 'copy'
monochrome_logs = false
help = false
version = false
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
// Config options
config_profile_name = null
config_profile_description = null
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
// Schema validation default options
validationFailUnrecognisedParams = false
validationLenientMode = false
validationSchemaIgnoreParams = 'genomes,igenomes_base'
validationShowHiddenParams = false
validate_params = true
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${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")
}
profiles {
debug {
dumpHashes = true
process.beforeScript = 'echo $HOSTNAME'
cleanup = false
nextflow.enable.configProcessNamesValidation = true
}
conda {
conda.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
conda.channels = ['conda-forge', 'bioconda', 'defaults']
apptainer.enabled = false
}
mamba {
conda.enabled = true
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
docker {
docker.enabled = true
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
docker.runOptions = '-u $(id -u):$(id -g)'
}
arm {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
conda.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
podman {
podman.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
shifter {
shifter.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
charliecloud {
charliecloud.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
apptainer.enabled = false
}
apptainer {
apptainer.enabled = true
apptainer.autoMounts = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
wave {
apptainer.ociAutoPull = true
singularity.ociAutoPull = true
wave.enabled = true
wave.freeze = true
wave.strategy = 'conda,container'
}
gitpod {
executor.name = 'local'
executor.cpus = 4
executor.memory = 8.GB
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
}
// Nextflow plugins
plugins {
id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
// 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"
}
process {
disk = 40.GB
withName: 'variantRecalibratorSNP|variantRecalibratorIndel|applyVQSRIndel|applyVQSRSNP|gatherVCF' {
container = 'broadinstitute/gatk:4.5.0.0'
}
//see conf/base.config for the performance options of defined by nf-core standards
withName: 'BCFTOOLS_FILTER|BCFTOOLS_NORM|BCFTOOLS_VIEW' {
errorStrategy = 'retry'
maxRetries = 1
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
disk = { check_max( 50.GB * task.attempt, 'disk' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
}
withName: 'COMBINEGVCFS' {
errorStrategy = 'retry'
maxRetries = 1
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
disk = { check_max( 80.GB * task.attempt, 'disk' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
}
withName: 'GATK4_GENOTYPEGVCFS' {
errorStrategy = 'retry'
maxRetries = 2
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 14.GB * task.attempt, 'memory' ) }
disk = { check_max( 40.GB * task.attempt, 'disk' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
}
withName: 'variantRecalibrator.*|apply.*' {
errorStrategy = 'retry'
maxRetries = 2
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 14.GB * task.attempt, 'memory' ) }
disk = { check_max( 30.GB * task.attempt, 'disk' ) }
time = { check_max( 10.h * task.attempt, 'time' ) }
}
withName: 'splitMultiAllelics' {
errorStrategy = 'retry'
maxRetries = 2
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 14.GB * task.attempt, 'memory' ) }
disk = { check_max( 30.GB * task.attempt, 'disk' ) }
time = { check_max( 10.h * task.attempt, 'time' ) }
}
withName: 'GATK4_VARIANTFILTRATION' {
errorStrategy = 'retry'
maxRetries = 2
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 14.GB * task.attempt, 'memory' ) }
disk = { check_max( 30.GB * task.attempt, 'disk' ) }
time = { check_max( 10.h * task.attempt, 'time' ) }
}
withName: 'TABIX_TABIX' {
errorStrategy = 'retry'
maxRetries = 2
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 14.GB * task.attempt, 'memory' ) }
disk = { check_max( 30.GB * task.attempt, 'disk' ) }
time = { check_max( 10.h * task.attempt, 'time' ) }
}
withName: 'ENSEMBLVEP_VEP' {
errorStrategy = 'retry'
maxRetries = 2
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
disk = { check_max( 80.GB * task.attempt, 'disk' ) }
time = { check_max( 10.h * task.attempt, 'time' ) }
}
withName: 'EXOMISER' {
errorStrategy = 'retry'
maxRetries = 2
cpus = { check_max( 6 * task.attempt, 'cpus' ) }
memory = { check_max( 36.GB * task.attempt, 'memory' ) }
disk = { check_max( 150.GB * task.attempt, 'disk' ) }
time = { check_max( 10.h * task.attempt, 'time' ) }
}
withName: 'writemeta' {
container = 'ubuntu:24.10'
}
}
// 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: $obj"
return obj
}
}
else if (type == 'disk') {
try {
if (obj.compareTo(params.max_disk as nextflow.util.MemoryUnit) == 1)
return params.max_disk as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max disk '${params.max_disk}' is not valid! Using default value: $obj"
return obj
}
}
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${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"
}
manifest {
name = 'ferlab/postprocessing'
author = """Damien Geneste, David Morais, Felix-Antoine Le Sieur, Jeremy Costanza, Lysiane Bouchard"""
homePage = 'https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline'
description = """Variant analysis for genome and exome GVCFs"""
mainScript = 'main.nf'
nextflowVersion = '!>=23.10.1'
version = '2.4.1-dev'
doi = ''
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'