/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    nf-core/airrflow Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Default config options for all compute environments
----------------------------------------------------------------------------------------
*/

// Global default params, used in configs
params {

    // Subworflow selection
    subworkflow = 'bcellmagic'

    // Input parameters
    input = null

    // Databases options
    igblast_base = null
    imgtdb_base = null
    save_databases = false

    // Bcellmagic specific options ---------

    // protocol options
    library_generation_method = null
    race_linker = null

    // Primer and UMI inputs
    index_file = null
    cprimers = null
    vprimers = null
    vprimer_start = 0
    cprimer_start = 0
    cprimer_position = 'R1'
    primer_revpr = false

    // UMI and primer handling
    umi_position = 'R1'
    umi_length = -1
    umi_start = 0

    // pRESTO options
    filterseq_q = 20
    primer_maxerror = 0.2
    primer_mask_mode = 'cut'
    primer_consensus = 0.6
    buildconsensus_maxerror = 0.1
    buildconsensus_maxgap = 0.5
    cluster_sets = true

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

    // Downstream analysis
    skip_report = false
    skip_lineage = false
    // -----------------------------------

    // Reveal specific options -----------
    collapseby = 'input_id'
    cloneby = 'subject_id'
    singlecell='single_cell'
    reassign = true
    productive_only = true
    remove_chimeric = true
    threshold = 'auto'
    miairr="$projectDir/assets/reveal/mapping_MiAIRR_BioSample_v1.3.1.tsv"

    // 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
    outdir = null
    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 = 'genomes,config_profile_name'
    enable_conda = false

    // Config options
    custom_config_version = 'master'
    custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
    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 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")
}

// Load nf-core/airrflow custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
// try {
//   includeConfig "${params.custom_config_base}/pipeline/airrflow.config"
// } catch (Exception e) {
//   System.err.println("WARNING: Could not load nf-core/config/airrflow profiles: ${params.custom_config_base}/pipeline/airrflow.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' }
    test_tcr_thr { includeConfig 'conf/test_tcr_thr.config' }
    test_no_umi { includeConfig 'conf/test_no_umi.config' }
    test_reveal { includeConfig 'conf/test_reveal.config' }
    test_reveal_no_cc { includeConfig 'conf/test_reveal_no_cc.config' }
    test_nocluster { includeConfig 'conf/test_nocluster.config' }
    test_fetchimgt { includeConfig 'conf/test_fetchimgt.config' }
}

// Load igenomes.config if required
if (!params.igenomes_ignore) {
    includeConfig 'conf/igenomes.config'
} else {
    params.genomes = [:]
}

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

// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.

env {
    PYTHONNOUSERSITE = 1
    R_PROFILE_USER   = "/.Rprofile"
    R_ENVIRON_USER   = "/.Renviron"
    JULIA_DEPOT_PATH = "/usr/local/share/julia"
}

// 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}.html"
}

manifest {
    name            = 'nf-core/airrflow'
    author          = 'Gisela Gabernet, Simon Heumos, Alexander Peltzer'
    homePage        = 'https://github.com/nf-core/airrflow'
    description     = 'B and T cell repertoire analysis pipeline with the Immcantation framework.'
    mainScript      = 'main.nf'
    nextflowVersion = '!>=21.10.3'
    version = '2.2.0'
}

// 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
        }
    }
}
