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nextflow.config
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nextflow.config
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// Please do not change the order of the numbered sections!
// The expected order is: 1. Parameters - 2. Profiles - 3. Process - 4. Executor
// There is a high chance it would break the configuration of 'profiles'
// 1. Parameters
// NOTE:
// Initialise the values of the params to the preferred default value or to false
docker.enabled = true
params {
// input options
gwas_summary_statistics = null
ld_reference_panel = "s3://twas-reference-files/1KG_phase3_v5_panel.gambit.tgz" // 1000Genomes phase 3 EUR LD panel
//eqtl_weights = "s3://twas-reference-files/PTWAS_scan.weights.hg38.txt.gz"
eqtl_weights = "s3://twas-data/PTWAS_scan.weights.small.hg38.txt.gz"
gambit_exec_path = "/GAMBIT/bin/GAMBIT"
outdir = 'results'
// report_dir is:
// - the folder from the container that includes the scripts for NF <= v20.01 (bin)
// - the ${projectDir}/bin folder of the root of the repo with the scripts for NF >= v20.10
report_dir = '/opt/bin/'
// when set to true, prints help and exits
help = false
// container for all processes, excluding those defined with 'withName' (see example below)
container = 'quay.io/lifebitai/ptwas:0.0.1_089aa00'
// process resources defaults
cpus = 1
memory = 2.GB
disk = '30.GB'
// max resources limits defaults
max_cpus = 2
max_memory = 4.GB
max_time = 8.h
// execution related defaults
config = 'conf/standard.config'
echo = false
errorStrategy = 'finish'
maxRetries = 9
maxForks = 200
queueSize = 200
executor = false
// google-lifesciences
gls_bootDiskSize = '50.GB'
gls_preemptible = true
zone = 'us-east1-b'
network = 'default'
subnetwork = 'default'
}
// 2. Profiles
// Do not update the order because the values set in params scope will not be overwritten
// Do not attempt to simplify to
// includeConfig params.config
// outside of profiles scope, it will fail to update the values of the params
profiles {
standard {includeConfig params.config}
docker { docker.enabled = true }
//base {includeConfig 'conf/base.config'}
//google {includeConfig 'conf/google.config'}
//test {includeConfig 'conf/test.config'}
//local {includeConfig 'conf/test.config'}
}
// 3. Process
// Do not change order of block, must follow after profiles scope (last section that updates params)
process {
echo = params.echo
cpus = params.cpus
memory = params.memory
maxRetries = params.maxRetries
maxForks = params.maxForks
container = params.container
errorStrategy = params.errorStrategy
withName: ptwas_scan {
disk = '60.GB'
cpus = 1
memory = '6.GB'
}
}
// 4. Executor - Do not remove this section! Required for running with different executors using --executor parameter
executor {
name = params.executor
queueSize = params.queueSize
}