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nextflow.config
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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
EBISPOT/gwas-sumstats-harmoniser Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// error strategy parameter
terminate_error = null
// global parameter
chromlist = null
chrom = null
ref = null
//reference preparation
reference = null
remote_vcf_location = null
remote_ensembl_variation = null
// External user running
harm = null
to_build = null
threshold = null
file = null
list = null
// GWAS catalog routine running
gwascatalog = null
all_harm_folder = null
inputPath = null
ftp = null
failed = null
// profile running
enable_conda = false
singularity_pull_docker_container = false
custom_config = null
}
includeConfig './config/basic.config'
includeConfig './config/container.config'
manifest {
name = 'EBISPOT/gwas-sumstats-harmoniser'
defaultBranch = 'nextflow'
homePage = 'https://github.com/EBISPOT/gwas-sumstats-harmoniser/'
mainScript = 'main.nf'
}
if (params.reference) {
if (!params.harm & !params.gwascatalog) {
includeConfig './config/reference.config'
if (params.chromlist){
params.chrom = params.chromlist?.tokenize(',') as List
}
}
}
if (params.harm) {
if (!params.reference & !params.gwascatalog) {
includeConfig './config/default_params.config'
includeConfig './config/basic.config'
if (params.chromlist){
params.chrom = params.chromlist?.tokenize(',') as List
}
}
}
if (params.gwascatalog) {
if (!params.harm & !params.reference) {
includeConfig './config/default_params.config'
includeConfig './config/basic.config'
includeConfig './config/gwascatalog.config'
}
}
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
test{
includeConfig './config/test.config'
}
standard {
process.executor = 'local'
}
executor {
includeConfig './config/executor.config'
if (params.terminate_error) {
includeConfig './config/exit_error.config'
} else{
includeConfig './config/ignore_error.config'
}
}
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
docker.runOptions = '-u $(id -u):$(id -g)'
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
}
gitpod {
executor.name = 'local'
executor.cpus = 16
executor.memory = 60.GB
}
}
if (params.custom_config) {
includeConfig params.custom_config
}