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

// Global default params, used in configs
params {

    // Input options
    input                        = null
    platform                     = null
    protocol                     = null

    // Reference genome options
    genome                       = null
    primer_set                   = null
    primer_set_version           = null
    primer_fasta                 = null
    primer_left_suffix           = '_LEFT'
    primer_right_suffix          = '_RIGHT'
    save_reference               = false

    // Nanopore options
    fastq_dir                    = null
    fast5_dir                    = null
    sequencing_summary           = null
    min_barcode_reads            = 100
    min_guppyplex_reads          = 10
    artic_minion_caller          = 'nanopolish'
    artic_minion_aligner         = 'minimap2'
    artic_minion_medaka_model    = null
    skip_pycoqc                  = false
    skip_nanoplot                = false

    // Nanopore/Illumina options
    asciigenome_read_depth       = 50
    asciigenome_window_size      = 50
    multiqc_title                = null
    multiqc_config               = null
    max_multiqc_email_size       = '25.MB'
    skip_mosdepth                = false
    skip_pangolin                = false
    skip_nextclade               = false
    skip_asciigenome             = false
    skip_variants_quast          = false
    skip_multiqc                 = false

    // Illumina QC, read trimming and filtering options
    kraken2_db                   = 's3://nf-core-awsmegatests/viralrecon/input_data/kraken2_human.tar.gz'
    kraken2_db_name              = 'human'
    kraken2_variants_host_filter = false
    kraken2_assembly_host_filter = true
    save_trimmed_fail            = false
    skip_fastqc                  = false
    skip_kraken2                 = false
    skip_fastp                   = false
    skip_cutadapt                = false

    // Illumina variant calling options
    callers                      = null
    min_mapped_reads             = 1000
    ivar_trim_noprimer           = false
    ivar_trim_offset             = null
    filter_duplicates            = false
    save_unaligned               = false
    save_mpileup                 = false
    skip_ivar_trim               = false
    skip_markduplicates          = true
    skip_picard_metrics          = false
    skip_snpeff                  = false
    skip_consensus               = false
    skip_variants                = false

    // Illumina de novo assembly options
    assemblers                   = 'spades'
    spades_mode                  = 'rnaviral'
    spades_hmm                   = null
    blast_db                     = null
    skip_bandage                 = false
    skip_blast                   = false
    skip_abacas                  = false
    skip_plasmidid               = false
    skip_assembly_quast          = false
    skip_assembly                = false

    // 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
    enable_conda                 = false
    singularity_pull_docker_container = false
    validate_params              = true
    show_hidden_params           = false
    schema_ignore_params         = 'genomes,modules,igenomes_base'

    // 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")
}

// Load nf-core/viralrecon custom config.
// The default 'genomes.config' used by the pipeline can be found here and is auto-loaded via the pipeline config:
// https://github.com/nf-core/configs/blob/master/conf/pipeline/viralrecon/genomes.config
try {
    includeConfig "${params.custom_config_base}/pipeline/viralrecon.config"
} catch (Exception e) {
    System.err.println("WARNING: Could not load nf-core/config/viralrecon profiles: ${params.custom_config_base}/pipeline/viralrecon.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_sispa         { includeConfig 'conf/test_sispa.config'         }
    test_nanopore      { includeConfig 'conf/test_nanopore.config'      }
    test_full          { includeConfig 'conf/test_full.config'          }
    test_full_illumina { includeConfig 'conf/test_full.config'          }
    test_full_nanopore { includeConfig 'conf/test_full_nanopore.config' }
    test_full_sispa    { includeConfig 'conf/test_full_sispa.config'    }
}

// Increase time available to build Conda environment
conda { createTimeout = "120 min" }

// 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/viralrecon'
    author          = 'Sarai Varona and Sara Monzon'
    homePage        = 'https://github.com/nf-core/viralrecon'
    description     = 'Assembly and intrahost/low-frequency variant calling for viral samples'
    mainScript      = 'main.nf'
    nextflowVersion = '!>=21.04.0'
    version         = '2.1'
}

// 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
        }
    }
}
