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

// Global default params, used in configs
params {

    // Input options
    input                           = null

    // QC and trimming options
    fastp_args                      = ""
    save_trimmed                    = false
    save_trimmed_fail               = false
    long_reads_filtering            = 'porechop'    // Allowed: ['porechop', 'filtlong']
    filtlong_minlen                 = 10
    filtlong_args                   = ""

    // Contamination_screening
    kraken2db                       = ''
    kmerfinderdb                    = ''
    reference_fasta                 = ''
    reference_gff                   = ''

    // Assembly parameters
    assembler                       = 'unicycler'   // Allowed: ['unicycler', 'canu', 'miniasm', 'dragonflye']
    assembly_type                   = null       // Allowed: ['short', 'long', 'hybrid'] (hybrid works only with Unicycler)
    unicycler_args                  = ""
    canu_mode                       = '-nanopore'   // Allowed: ['-pacbio', '-nanopore', '-pacbio-hifi']
    canu_args                       = ''            // Default no extra options, can be adjusted by the user
    dragonflye_args                 = ''

    // Assembly polishing
    polish_method                   = 'medaka'      // Allowed: ['medaka', 'nanopolish']

    // Assembly QC
    busco_lineage                   = 'bacteria_odb10'
    busco_mode                      = 'genome'
    busco_db_path                   =  null
    busco_config_file 		        =  null
    busco_clean_intermediates 	    = false

    // Annotation
    annotation_tool                 = 'prokka'      // Allowed: ['prokka', 'bakta', 'dfast', 'liftoff']
    prokka_args                     = ""
    prokka_proteins                 = ''
    baktadb                         = ''
    baktadb_download                = false
    baktadb_download_args           = '--type light' // Allowed: ['--type light', '--type full']
    dfast_config                    = "$projectDir/assets/test_config_dfast.py"
    liftoff_ref_from_kmerfinder     = false  // use reference for liftoff from kmerfinder output

    // Skipping options
    skip_fastqc                     = false
    skip_nanoplot                   = false
    skip_toulligqc                  = false
    skip_fastp                      = false
    discard_trimmed_pass            = false
    skip_kraken2                    = false
    skip_kmerfinder                 = false
    skip_pycoqc                     = false
    skip_busco 			    = false
    skip_annotation                 = false
    skip_polish                     = false
    skip_multiqc                    = false

    // MultiQC options
    multiqc_config             = null
    multiqc_title              = null
    multiqc_logo               = null
    max_multiqc_email_size     = '25.MB'
    multiqc_methods_description = null

    // Boilerplate options
    outdir                       = null
    publish_dir_mode             = 'copy'
    email                        = null
    email_on_fail                = null
    plaintext_email              = false
    monochrome_logs              = false
    hook_url                     = null
    help                         = false
    help_full                    = false
    show_hidden                  = false
    version                      = false
    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
    trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// Config options
    config_profile_name        = null
    config_profile_description = null

    custom_config_version      = 'master'
    custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
    config_profile_contact     = null
    config_profile_url         = null

    // Schema validation default options
    validate_params            = true
}

// Load base.config by default for all pipelines
includeConfig 'conf/base.config'

profiles {
    debug {
        dumpHashes              = true
        process.beforeScript    = 'echo $HOSTNAME'
        cleanup                 = false
        nextflow.enable.configProcessNamesValidation = true
    }
    conda {
        conda.enabled           = true
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        conda.channels          = ['conda-forge', 'bioconda']
        apptainer.enabled       = false
    }
    mamba {
        conda.enabled           = true
        conda.useMamba          = true
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
    }
    docker {
        docker.enabled          = true
        conda.enabled           = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
        docker.runOptions       = '-u $(id -u):$(id -g)'
    }
    arm {
        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
    }
    singularity {
        singularity.enabled     = true
        singularity.autoMounts  = true
        conda.enabled           = false
        docker.enabled          = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
    }
    podman {
        podman.enabled          = true
        conda.enabled           = false
        docker.enabled          = false
        singularity.enabled     = false
        shifter.enabled         = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
    }
    shifter {
        shifter.enabled         = true
        conda.enabled           = false
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        charliecloud.enabled    = false
        apptainer.enabled       = false
    }
    charliecloud {
        charliecloud.enabled    = true
        conda.enabled           = false
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        apptainer.enabled       = false
    }
    apptainer {
        apptainer.enabled       = true
        apptainer.autoMounts    = true
        conda.enabled           = false
        docker.enabled          = false
        singularity.enabled     = false
        podman.enabled          = false
        shifter.enabled         = false
        charliecloud.enabled    = false
    }
    wave {
        apptainer.ociAutoPull   = true
        singularity.ociAutoPull = true
        wave.enabled            = true
        wave.freeze             = true
        wave.strategy           = 'conda,container'
    }
    gitpod {
        executor.name           = 'local'
        executor.cpus           = 4
        executor.memory         = 8.GB
        process {
            resourceLimits = [
                memory: 8.GB,
                cpus  : 4,
                time  : 1.h
            ]
        }
    }
    gpu {
        docker.runOptions       = '-u $(id -u):$(id -g) --gpus all'
        apptainer.runOptions    = '--nv'
        singularity.runOptions  = '--nv'
    }
    test                     { includeConfig 'conf/test.config'                    }
    test_dfast               { includeConfig 'conf/test_dfast.config'              }
    test_liftoff             { includeConfig 'conf/test_liftoff.config'            }
    test_hybrid              { includeConfig 'conf/test_hybrid.config'             }
    test_hybrid_dragonflye   { includeConfig 'conf/test_hybrid_dragonflye.config'  }
    test_long                { includeConfig 'conf/test_long.config'               }
    test_long_miniasm        { includeConfig 'conf/test_long_miniasm.config'       }
    test_long_miniasm_prokka { includeConfig 'conf/test_long_miniasm_prokka.config'}
    test_long_dragonflye     { includeConfig 'conf/test_long_dragonflye.config'    }
    test_full                { includeConfig 'conf/test_full.config'               }
}

// Load nf-core custom profiles from different institutions

// If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included.
// Load nf-core/bacass custom profiles from different institutions.
includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"


// Load nf-core/bacass custom profiles from different institutions.
// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/bacass.config" : "/dev/null"

// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry    = 'quay.io'
docker.registry       = 'quay.io'
podman.registry       = 'quay.io'
singularity.registry  = 'quay.io'
charliecloud.registry = 'quay.io'



// 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"
}

// Set bash options
process.shell = [
    "bash",
    "-C",         // No clobber - prevent output redirection from overwriting files.
    "-e",         // Exit if a tool returns a non-zero status/exit code
    "-u",         // Treat unset variables and parameters as an error
    "-o",         // Returns the status of the last command to exit..
    "pipefail"    //   ..with a non-zero status or zero if all successfully execute
]

// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false

timeline {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html"
}
report {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html"
}
trace {
    enabled = true
    file    = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt"
}
dag {
    enabled = true
    file    = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html"
}

manifest {
    name            = 'nf-core/bacass'
    contributors    = [
        [
            name: 'Andreas Wilm',
            affiliation: '',
            email: '',
            github: 'andreas-wilm',
            contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: ''
        ],
        [
            name: 'Alexander Peltzer',
            affiliation: '',
            email: '',
            github: 'apeltzer',
            contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor')
            orcid: ''
        ],
        [
            name: 'Daniel Straub',
            affiliation: 'Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany',
            email: '',
            github: 'd4straub',
            contribution: ['maintainer'],
            orcid: '0000-0002-2553-0660 ',
        ],
        [
            name: 'Daniel Valle-Millares',
            affiliation: 'Bioinformatics Platform, CIBER thematic area of Infectious Diseases (CIBERINFEC), Madrid, Spain',
            email: '',
            github: 'Daniel-VM',
            contribution: ['maintainer'],
            orcid: '0000-0002-5205-855X ',
        ],
    ]
    homePage        = 'https://github.com/nf-core/bacass'
    description     = """Simple bacterial assembly and annotation"""
    mainScript      = 'main.nf'
    defaultBranch   = 'main'
    nextflowVersion = '!>=24.10.5'
    version         = '2.5.0'
    doi             = '10.5281/zenodo.2669428'
}

// Nextflow plugins
plugins {
    id 'nf-schema@2.4.2' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}

validation {
    defaultIgnoreParams = ["genomes"]
    monochromeLogs = params.monochrome_logs
    help {
        enabled = true
        command = "nextflow run nf-core/bacass -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
        fullParameter = "help_full"
        showHiddenParameter = "show_hidden"
        beforeText = """
-\033[2m----------------------------------------------------\033[0m-
                                        \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
\033[0;34m        ___     __   __   __   ___     \033[0;32m/,-._.--~\'\033[0m
\033[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \033[0;33m}  {\033[0m
\033[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \033[0;32m\\`-._,-`-,\033[0m
                                        \033[0;32m`._,._,\'\033[0m
\033[0;35m  nf-core/bacass ${manifest.version}\033[0m
-\033[2m----------------------------------------------------\033[0m-
"""
        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
* The nf-core framework
    https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
    https://github.com/nf-core/bacass/blob/main/CITATIONS.md
"""
    }
    summary {
        beforeText = validation.help.beforeText
        afterText = validation.help.afterText
    }
}

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