/*

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

    nf-core/deepmodeloptim Nextflow config file

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

    Default config options for all compute environments

----------------------------------------------------------------------------------------

*/

// Global default params, used in configs

params {

    // Input options

    data                    = null // TODO either change one of the params above by input or create a samplesheet containing the info of them

    model                   = null                   // the model file in python, the model that will be tested by this pipeline

    data_config             = null                   // the config file that specifies all the parameters relative to the data manipulation

    model_config            = null                   // the config file with all the hyperparameter directives (choiches) and all ray tune specs

    preprocessing_config    = null                   // the config file that specifies the data preprocessing steps

    // Optional inputs

    initial_weights         = null                   // the initial weights of the model. These files can be used to start the training instead of random initialization. One can provide several files, each of them will be used for a different run.

    // Input options for data preprocessing protocols

    genome                  = null

    igenomes_base           = 's3://ngi-igenomes/igenomes/'

    bed_peak_size           = 300                   // the size of the region around the peak that will be centered

    // Tuning options

    tune_trials_range       = null                  // the number of trials for the tuning step e.g. "10,20,5" will do 10, 15 and 20 trials

    tune_replicates         = 1                     // the number of replicates for each trial #

    prediction_data         = null                  // the file with the data to predict for evaluation purposes

    // Output options

    outdir                  = "./results/"          // the outdir has to be the one the user specify _ the unique name of the run _ the time so that multiple runs will not overlap

    publish_dir_mode        = "copy"

    save_data               = false                 // save transformed data or not

    // Computational resources

    max_gpus                = 1                      // requesting the gpus for the tuning steps.

    // TODO this should not be in the nextflow config but in each config

    // max_cpus                = 12                      // this flasg and the following are for regulating resources, profiles can overwrite these.

    // max_memory              = 32.GB

    // max_time                = "72.h"

    // Error options

    max_retries             = 0

    err_start               = 'finish'

    // Optional flags

    check_model             = true                   // flag to tell whether to check or not if the model can be tuned and trained. It does one call of the batch function, (predicting), of the model importing and using everything needed for that. Default run such a check.

    check_model_num_samples = null                   // optional flag to do a more extensive check during check_model. This will override user given num_sample value for the tune run. This will give the user control on how extensive it wants the check to be.

    shuffle                 = true                   // flag to tell wether to shuffle or not the data and run a train on it. Sanity check always run on default. (If the way we think at shuffle change maybe is better to remove this flag and make it into a parameter of the user given json for noise nad split)

    debug_mode              = false                  // flag used to switch to debug mode for the pipeline.

    // Development stage options

    // please change them in dev.config

    container_dev           = null

    // General

    help                    = false

    validate_params         = true                     // tells wether or not to validate input values using nf-schema.

    // 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

            ]

        }

    }

    test         { includeConfig "conf/test.config"       }

    test_stub    { includeConfig "conf/test_stub.config"  }

    test_ibis    { includeConfig "conf/test_ibis.config"  }

    test_ibis_with_preprocessing { includeConfig "conf/test_ibis_with_preprocessing.config" }

    test_noise_eval { includeConfig "conf/test_noise_eval.config" }

    local        { includeConfig "conf/local.config"      }

    dev          { includeConfig "conf/dev.config"        }

}

// Load nf-core custom profiles from different Institutions

includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"

// Load igenomes.config if required

if (params.genome == null) {

    params.genomes = [:]

} else {

    includeConfig 'conf/igenomes.config'

}

// Load nf-core/deepmodeloptim custom profiles from different institutions.

// TODO This line can be uncommented once you move the pipeline to nf-core. A file deepmodeloptim.config will be automatically created at the nf-core/configs repo. This is to allow having a pipeline specific config.

// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/deepmodeloptim.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/deepmodeloptim'

    author          = """Mathys Grapotte""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead

    contributors    = [

        // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0

        [

            name: 'Mathys Grapotte',

            affiliation: '',

            email: '',

            github: '',

            contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')

            orcid: ''

        ],

    ]

    homePage        = 'https://github.com/nf-core/deepmodeloptim'

    description     = """nf-core/deepmodeloptim is an end-to-end pipeline designed to facilitate the testing and development of deep learning models for genomics."""

    mainScript      = 'main.nf'

    defaultBranch   = 'master'

    nextflowVersion = '!>=24.04.2'

    version         = '1.0.0dev'

    doi             = ''

}

// Nextflow plugins

plugins {

    id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet

}

validation {

    defaultIgnoreParams = ["genomes", "data", "data_config", "model_config"]

    monochromeLogs = params.monochrome_logs

    help {

        enabled = true

        command = "nextflow run nf-core/deepmodeloptim -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/deepmodeloptim ${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/deepmodeloptim/blob/master/CITATIONS.md

"""

    }

    summary {

        beforeText = validation.help.beforeText

        afterText = validation.help.afterText

    }

}

// Load modules.config for DSL2 module specific options

includeConfig 'conf/modules.config'