/*

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

    Config file for defining DSL2 per module options and publishing paths

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

    Available keys to override module options:

        ext.args   = Additional arguments appended to command in module.

        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).

        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).

        ext.prefix = File name prefix for output files.

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

*/

process {

    // ==============================================================================

    // config for preprocess_ibis_bedfile_to_stimulus

    // ==============================================================================

    withName: "CENTER_AROUND_PEAK" {

        publishDir = [

            enabled: false

        ]

        ext.args   = { "-v N=${params.bed_peak_size}" }

        ext.prefix = { "${meta.id}.centered" }

        ext.suffix = { "bed" }

    }

    withName: "EXTRACT_FOREGROUND" {

        publishDir = [

            enabled: false

        ]

        ext.args = {[

            separator: '\t'

        ]}

        ext.prefix = { "${meta.id}.foreground" }

    }

    withName: "EXTRACT_BACKGROUND_ALIENS" {

        publishDir = [

            enabled: false

        ]

        ext.args = {[

            separator: '\t'

        ]}

        ext.prefix = { "${meta.id}.background_aliens" }

    }

    withName: "EXTRACT_BACKGROUND_SHADE" {

        publishDir = [

            enabled: false

        ]

        ext.args = {[

            meta.shade_args ? "${meta.shade_args}" : '',

            "| awk '\$3 - \$2 >= ${params.bed_peak_size}'",  // keep only the peaks that have certain size

        ].join(' ').trim()}

        ext.prefix = { "${meta.id}.background_shade" }

    }

    withName: "EXTRACT_BACKGROUND_SHUFFLE" {

        publishDir = [

            enabled: false

        ]

        ext.prefix = { "${meta.id}.background_shuffle" }

    }

    withName: "BEDTOOLS_SUBTRACT" {

        publishDir = [

            enabled: false

        ]

        ext.prefix = { "${meta.id}.background_${meta.background_type}.clean" }

        ext.args = {"-A"} // remove entire feature if any overlap

    }

    withName: "BACKGROUND_FOREGROUND_TO_STIMULUS_CSV" {

        publishDir = [

            path: {"${params.outdir}/data"},

            mode: params.publish_dir_mode,

            pattern: "*.csv",

            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }

        ]

        ext.prefix = { "${meta.id}.stimulus" }

        ext.suffix = { "csv" }

        ext.args = {[

            "-v column_name=background_type",

            "-v column_value=${meta.background_type}"

        ].join(' ').trim()}

    }

    // ==============================================================================

    // main config

    // ==============================================================================

    withName: "STIMULUS_SPLIT_TRANSFORM" {

        publishDir = [

            path: { "${params.outdir}/configs/${meta.id}" },

            mode: params.publish_dir_mode,

            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }

        ]

        tag = { "${meta.id}" }

        if (params.container_dev) {

            container = params.container_dev

        }

    }

    withName: "STIMULUS_SPLIT_DATA" {

        publishDir = [

            enabled: false

        ]

        ext.prefix = { "${meta.id}-split-${meta.split_id}" }

        tag = { "${meta.id} - split: ${meta.split_id}" }

        if (params.container_dev) {

            container = params.container_dev

        }

    }

    withName: "STIMULUS_TRANSFORM_CSV" {

        publishDir = [

            path: { "${params.outdir}/transformed_data/${meta.id}" },

            mode: params.publish_dir_mode,

            when: params.save_data,

            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }

        ]

        ext.prefix = { "${meta.id}-split-${meta.split_id}-trans-${meta.transform_id}" }

        tag = { "${meta.id} - split: ${meta.split_id} - transform: ${meta.transform_id}" }

        if (params.container_dev) {

            container = params.container_dev

        }

    }

    withName: "CHECK_MODEL" {

        ext.args = { [

            params.check_model_num_samples ? "-n ${params.check_model_num_samples}" : '',

            params.debug_mode ? "--debug_mode" : ''

        ].flatten().unique(false).join(' ').trim()}

        tag = { "${meta.id} - split: ${meta.split_id} - transform: ${meta.transform_id}" }

        if (params.container_dev) {

            container = params.container_dev

        }

    }

    withName: "STIMULUS_TUNE" {

        ext.args = { [

            params.debug_mode ? "--debug_mode" : ''

        ].flatten().unique(false).join(' ').trim()}

        publishDir = [

            path: { "${params.outdir}/tune_results/${meta.id}/${meta.split_id}/${meta.transform_id}" },

            mode: params.publish_dir_mode,

            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }

        ]

        ext.prefix = { "${meta.id}-split-${meta.split_id}-trans-${meta.transform_id}-rep-${meta.replicate}" }

        tag = { "${meta.id} - split: ${meta.split_id} - transform: ${meta.transform_id} - replicate: ${meta.replicate}" }

        if (params.container_dev) {

            container = params.container_dev

        }

    }

    withName: "STIMULUS_PREDICT" {

        ext.prefix = { "${meta.id}-split-${meta.split_id}-transf-${meta.transform_id}-rep-${meta.replicate}" }

        tag = { "${meta.id} - split: ${meta.split_id} - transform: ${meta.transform_id} - replicate: ${meta.replicate}" }

        if (params.container_dev) {

            container = params.container_dev

        }

    }

    withName: "STIMULUS_COMPARE_TENSORS_COSINE" {

        ext.args = { "--mode cosine_similarity" }

        if (params.container_dev) {

            container = params.container_dev

        }

    }

    withName: "CONCAT_COSINE" {

        ext.prefix = { "summary_cosine" }

        publishDir = [

            path: { "${params.outdir}/evaluation_results/" },

            mode: params.publish_dir_mode,

            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }

        ]

    }

}