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

// Global default params, used in configs
params {

    // Input parameters
    input = null
    index_file = false
    cprimers = null
    vprimers = null

    // Databases options
    igblast_base = false
    imgtdb_base = false
    species = 'human'
    loci = 'ig'
    save_databases = false

    // protocol options
    protocol = 'pcr_umi'
    race_linker = null

    // UMI and primer handling
    umi_position = 'R1'
    umi_length = 0
    umi_start = 0
    vprimer_start = 0
    cprimer_start = 0
    cprimer_position = 'R1'
    primer_maxerror = 0.2
    primer_mask_mode = 'cut'
    primer_consensus = 0.6

    // PRESTO options
    filterseq_q = 20

    // Clustering parameters
    set_cluster_threshold = false
    cluster_threshold = 0.14
    threshold_method = 'density'

    // Downstream analysis
    skip_report = false
    skip_lineage = false

    // References
    igenomes_base = 's3://ngi-igenomes/igenomes'
    igenomes_ignore = true

    // MultiQC options
    multiqc_config = null
    multiqc_title = null
    max_multiqc_email_size = 25.MB
    skip_multiqc = false

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

    // Config options
    custom_config_version = 'master'
    custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
    hostnames = [:]
    config_profile_name = null
    config_profile_description = null
    config_profile_contact = null
    config_profile_url = 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'

// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.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 {
    conda {
        params.enable_conda = true
        docker.enabled = false
        singularity.enabled = false
        podman.enabled = false
        shifter.enabled = false
        charliecloud.enabled = false
    }
    debug { process.beforeScript = 'echo $HOSTNAME' }
    docker {
        docker.enabled = true
        singularity.enabled = false
        podman.enabled = false
        shifter.enabled = false
        charliecloud.enabled = false
        docker.runOptions = '-u $(id -u):$(id -g)'
    }
    singularity {
        singularity.enabled = true
        singularity.autoMounts = true
        docker.enabled = false
        podman.enabled = false
        shifter.enabled = false
        charliecloud.enabled = false
    }
    podman {
        podman.enabled = true
        singularity.enabled = false
        docker.enabled = false
        shifter.enabled = false
        charliecloud.enabled = false
    }
    shifter {
        shifter.enabled = true
        singularity.enabled = false
        docker.enabled = false
        podman.enabled = false
        charliecloud.enabled = false
    }
    charliecloud {
        charliecloud.enabled = true
        singularity.enabled = false
        docker.enabled = false
        podman.enabled = false
        shifter.enabled = false
    }
    test { includeConfig 'conf/test.config' }
    test_full { includeConfig 'conf/test_full.config' }
    test_tcr { includeConfig 'conf/test_tcr.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"
}

manifest {
    name            = 'nf-core/bcellmagic'
    author          = 'Gisela Gabernet, Simon Heumos, Alexander Peltzer'
    homePage        = 'https://github.com/nf-core/bcellmagic'
    description     = 'B and T cell repertoire analysis pipeline with the Immcantation framework.'
    mainScript      = 'main.nf'
    nextflowVersion = '!>=21.04.0'
    version         = '2.0.0'
}

// 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
        }
    }
}
