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nextflow.config
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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/gwas Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
//------------------------
// TODO: h3abionet qc params
//------------------------
// Input options
input = null
// Directories
work_dir = "$PWD"
input_dir = "sample"
// Can use S3 too
//input_dir = "s3://h3abionet/sample"
input_pat = "sampleA"
output_dir = "${params.work_dir}/output"
scripts = "${params.work_dir}/scripts"
output = "out"
max_forks = 95
high_ld_regions_fname = ""
sexinfo_available = true
cut_het_high = 0.343
cut_het_low = 0.15
cut_diff_miss = "0.05"
cut_maf = "0.01"
cut_mind = "0.02"
cut_geno = 0.01
cut_hwe = 0.008
pi_hat = 0.11
super_pi_hat = 0.7
f_lo_male = 0.8 // default for F-sex check -- >= means male
f_hi_female = 0.2 // <= means female
gc10 = 0.4 // 10% Gen Call confidence -- 0.4 is very low
case_control = "${params.input_dir}/sample.phe"
case_control_col = "PHE"
idpat = 0 // or "(\\w+)-DNA_(\\w+)_.*" or ".*_(.*)"
plink_mem_req = "1750MB"
other_mem_req = "1750MB"
big_time = '12h'
sharedStorageMount = "/mnt/shared"
max_plink_cores = 4
// // Set in QC subworkflow
phenotype = "0"
pheno_col = ""
batch = "0"
batch_col = 0
samplesheet = "0"
// queue = 'batch'
remove_on_bp = 1
//------------------------
// nf-core: Specify your pipeline's command line flags
//------------------------
// References
genome = null
igenomes_base = 's3://ngi-igenomes/igenomes'
igenomes_ignore = 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 = null
tracedir = "${params.outdir}/pipeline_info"
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
version = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes'
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${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'
// FIXME 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: ${params.custom_config_base}/nfcore_custom.config")
// }
// FIXME Load nf-core/gwas custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
// try {
// includeConfig "${params.custom_config_base}/pipeline/gwas.config"
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/gwas profiles: ${params.custom_config_base}/pipeline/gwas.config")
// }
profiles {
debug {
dumpHashes = true
process.beforeScript = 'echo $HOSTNAME'
cleanup = false
}
conda {
conda.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
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
docker.registry = 'quay.io'
docker.userEmulation = true
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
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
podman.registry = 'quay.io'
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
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.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' }
//====================================
qc_wf {
executor {
queueSize = 5
pollInterval = '5sec'
}
process {
executor = 'slurm'
queue = 'hsw-fdr'
container = "quay.io/h3abionet_org/py3plink"
withLabel: latex {
container = "quay.io/h3abionet_org/h3agwas-texlive"
}
withLabel: py2fast {
container = "quay.io/h3abionet_org/py2fastlmm"
}
}
}
//====================================
}
// 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 = "${params.tracedir}/execution_timeline_${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/gwas'
author = """Davi Josué Marcon (@Mxrcon), Abhinav Sharma (@abhi18av), Jean-Tristan Brandenburg (@jeantristanb), Lindsay Clark (@lvclark) and Scott Hazelhurst (@shaze)."""
homePage = 'https://github.com/nf-core/gwas'
description = """A pipeline for genome wide association studies."""
mainScript = 'main.nf'
nextflowVersion = '!>=22.10.1'
version = '1.0dev'
doi = ''
}
// 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
}
}
}