nextflow.config

/*
========================================================================================
    nf-core/scflow Nextflow config file
========================================================================================
    Default config options for all compute environments
----------------------------------------------------------------------------------------
*/

manifest {
    name = 'nf-core/scflow'
    author = 'Dr Combiz Khozoie'
    homePage = 'https://github.com/nf-core/scflow'
    description = 'Complete analysis workflow for single-cell/nuclei RNA-sequencing data.'
    mainScript = 'main.nf'
    nextflowVersion = '>=21.04.2'
    version = '1.0.0'
}

// Container slug. Stable releases should specify release tag!
// Developmental code should specify :dev
process.container = 'almurphy/scfdev:0.7.1'

//workDir = "/rds/general/user/$USER/ephemeral/tmp"
workDir = './work'

// Global default params, used in configs
params {
    // nf-core-scflow Workflow flags
    manifest = './refs/Manifest.txt'
    input = './refs/SampleSheet.tsv'
    ensembl_mappings = './src/ensembl-ids/ensembl_mappings.tsv'
    ctd_path = 'https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/28033407/ctd_v1.zip'
    celltype_mappings = './conf/celltype_mappings.tsv'
    reddim_genes_yml = './conf/reddim_genes.yml'

    // Boilerplate options
    outdir                     = './results'
    tracedir                   = "${params.outdir}/pipeline_info"
    publish_dir_mode           = 'copy'
    email                      = null
    email_on_fail              = null
    plaintext_email            = false
    monochrome_logs            = false
    help                       = false
    validate_params            = true
    show_hidden_params         = false
    schema_ignore_params       = 'input,modules'
    enable_conda               = false
    singularity_pull_docker_container = false

    // Config options
    custom_config_version      = 'master'
    custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
    hostnames                  = [:]
    config_profile_description = null
    config_profile_contact     = null
    config_profile_url         = null
    config_profile_name        = null
    validate_params            = true
    show_hidden_params         = false
    schema_ignore_params       = 'modules,genome,input'

    // 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'

// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'

// SCFLOW DEFAULT ANALYSIS PARAMETERS
includeConfig 'conf/scflow_analysis.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 { process.beforeScript = 'echo $HOSTNAME' }
    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
        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
    }
    test      { includeConfig 'conf/test.config'      }
    test_full { includeConfig 'conf/test_full.config' }
}

// Export these variables to prevent local Python/R libraries from conflicting with those in the container
env {
    PYTHONNOUSERSITE = 1
    R_PROFILE_USER   = '/.Rprofile'
    R_ENVIRON_USER   = '/.Renviron'
}

// 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}.svg"
}

// 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
        }
    }
}