heart_rate_tmp_simulation_gxg/nextflow.config at main · birneylab/heart_rate_tmp_simulation_gxg · GitHub

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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Default config options
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Author: Saul Pierotti
Mail: saul@ebi.ac.uk
----------------------------------------------------------------------------------------
*/

manifest {
    author = "Saul Pierotti"

    // raise a warning if using a different nextflow version than the one used in the
    // development of the pipeline
    nextflowVersion = "24.10.5"
}

// short name of the project, used also for prefixing the results and cache
manifest.name = "heart_rate_tmp_simulation_gxg"

// Configuration via labels
process {
    withLabel: "r_tidyverse_datatable" {
        // add pgenlibr manually to env since not on conda
        conda = "r-base=4.2.3 r-tidyverse=2.0.0  r-data.table=1.14.8  r-r.utils=2.12.3"
    }
    withLabel: "r_gaston" {
        conda = "r-gaston=1.6"
    }
    withLabel: "plink2" {
        conda = "bioconda::plink2=2.00a5"
    }
    withName: "get_formulas" {
        publishDir = [
            path: { "${params.outdir}/" },
            mode: 'copy',
        ]
    }
    withName: "read_pheno_covar" {
        publishDir = [
            path: { "${params.outdir}/" },
            mode: 'copy',
        ]
    }
    withName: "make_pgen" {
        memory = "10 GB"
        publishDir = [
            path: { "${params.outdir}/pgen" },
            mode: 'copy',
        ]
    }
    withName: "get_qtl_matrices" {
        publishDir = [
            path: { "${params.outdir}/matrices" },
            mode: 'copy',
        ]
    }
    withName: "fit_mixed_model" {
        publishDir = [
            path: { "${params.outdir}/mixed_model" },
            mode: 'copy',
        ]
    }
    withName: "fit_lm" {
        publishDir = [
            path: { "${params.outdir}/lm" },
            mode: 'copy',
        ]
    }
    withName: "simulate" {
        publishDir = [
            path: { "${params.outdir}/simulation/${meta.locus_id}/" },
            mode: 'copy',
            pattern: "*.simulated_data.rds"
        ]
        time = { 36.hour * task.attempt }
        memory = { 50.GB * task.attempt }
        maxForks = 200
    }
    withName: "aggregate_results" {
        publishDir = [
            path: { "${params.outdir}/results" },
            mode: 'copy',
        ]
    }

    cpus   = { 1    * task.attempt }
    memory = { 6.GB * task.attempt }
    time   = { 4.h  * task.attempt }
    errorStrategy  = "retry"
    maxRetries = 3
}

params {
    outdir = "/nfs/research/birney/users/saul/nextflow/${manifest.name}"
    storedir = "/hps/nobackup/birney/users/saul/nextflow_storedir/${manifest.name}"
    pheno = null
    covar = null
    qtls = null
    freq = null
    vcf = null
    temperature_file = null
    n_chr = null
    n_rep = null
    n_samples = null
    allele_freq = null
    random_seed = 1
    noise_levels = null
    r2 = null
    temperature_trans = "x"
    heart_rate_trans = "x"
}