//
// Subworkflow with functionality specific to the nf-core/airrflow pipeline
//

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin'
include { paramsSummaryMap          } from 'plugin/nf-validation'
include { fromSamplesheet           } from 'plugin/nf-validation'
include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
include { dashedLine                } from '../../nf-core/utils_nfcore_pipeline'
include { nfCoreLogo                } from '../../nf-core/utils_nfcore_pipeline'
include { imNotification            } from '../../nf-core/utils_nfcore_pipeline'
include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
include { workflowCitation          } from '../../nf-core/utils_nfcore_pipeline'

/*
========================================================================================
    SUBWORKFLOW TO INITIALISE PIPELINE
========================================================================================
*/

workflow PIPELINE_INITIALISATION {

    take:
    version           // boolean: Display version and exit
    help              // boolean: Display help text
    validate_params   // boolean: Boolean whether to validate parameters against the schema at runtime
    monochrome_logs   // boolean: Do not use coloured log outputs
    nextflow_cli_args //   array: List of positional nextflow CLI args
    outdir            //  string: The output directory where the results will be saved
    input             //  string: Path to input samplesheet

    main:

    ch_versions = Channel.empty()

    //
    // Print version and exit if required and dump pipeline parameters to JSON file
    //
    UTILS_NEXTFLOW_PIPELINE (
        version,
        true,
        outdir,
        workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
    )

    //
    // Validate parameters and generate parameter summary to stdout
    //
    pre_help_text = nfCoreLogo(monochrome_logs)
    post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs)
    def String workflow_command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
    UTILS_NFVALIDATION_PLUGIN (
        help,
        workflow_command,
        pre_help_text,
        post_help_text,
        validate_params,
        "nextflow_schema.json"
    )

    //
    // Check config provided to the pipeline
    //
    UTILS_NFCORE_PIPELINE (
        nextflow_cli_args
    )
    //
    // Custom validation for pipeline parameters
    //
    validateInputParameters()

    //
    // Create channel from input file provided through params.input
    //
    ch_samplesheet = Channel.fromPath(input, checkIfExists: true)

    emit:
    samplesheet = ch_samplesheet
    versions    = ch_versions
}

/*
========================================================================================
    SUBWORKFLOW FOR PIPELINE COMPLETION
========================================================================================
*/

workflow PIPELINE_COMPLETION {

    take:
    email           //  string: email address
    email_on_fail   //  string: email address sent on pipeline failure
    plaintext_email // boolean: Send plain-text email instead of HTML
    outdir          //    path: Path to output directory where results will be published
    monochrome_logs // boolean: Disable ANSI colour codes in log output
    hook_url        //  string: hook URL for notifications
    multiqc_report  //  string: Path to MultiQC report

    main:

    summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")

    //
    // Completion email and summary
    //
    workflow.onComplete {
        if (email || email_on_fail) {
            completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList())
        }

        completionSummary(monochrome_logs)

        if (hook_url) {
            imNotification(summary_params, hook_url)
        }
    }

    workflow.onError {
        log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting"
    }
}

/*
========================================================================================
    FUNCTIONS
========================================================================================
*/
//
// Check and validate pipeline parameters
//
def validateInputParameters() {
    genomeExistsError()
}

//
// Validate channels from input samplesheet
//
def validateInputSamplesheet(input) {
    def (metas, fastqs) = input[1..2]

    // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end
    def endedness_ok = metas.collect{ it.single_end }.unique().size == 1
    if (!endedness_ok) {
        error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}")
    }

    return [ metas[0], fastqs ]
}
//
// Get attribute from genome config file e.g. fasta
//
def getGenomeAttribute(attribute) {
    if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
        if (params.genomes[ params.genome ].containsKey(attribute)) {
            return params.genomes[ params.genome ][ attribute ]
        }
    }
    return null
}

//
// Exit pipeline if incorrect --genome key provided
//
def genomeExistsError() {
    if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
        def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
            "  Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
            "  Currently, the available genome keys are:\n" +
            "  ${params.genomes.keySet().join(", ")}\n" +
            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
        error(error_string)
    }
}

//
// Generate methods description for MultiQC
//
def toolCitationText() {
    // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "",
    // Uncomment function in methodsDescriptionText to render in MultiQC report
    def citation_text = [
            "Tools used in the workflow included:",
            "pRESTO (Vander Heiden et al. 2014),",
            "IgBLAST (Ye et al. 2013),",
            "Alakazam (Stern et al. 2014),",
            "Shazam (Gupta et al. 2015),",
            "Change-O (Gupta et al. 2015),",
            "SCOPer (Gupta et al. 2017, Nouri et al. 2018),",
            "Dowser (Hoehn et al. 2022),",
            "IgPhyML (Hoehn et al. 2019)",
            "FastQC (Andrews 2010),",
            "MultiQC (Ewels et al. 2016)",
            "Fastp (Chen et al. 2018),",
            "."
        ].join(' ').trim()

    return citation_text
}

def toolBibliographyText() {
    // Add bibliographic entries to this list.
    // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "<li>Author (2023) Pub name, Journal, DOI</li>" : "",
    // Uncomment function in methodsDescriptionText to render in MultiQC report
    def reference_text = [
            "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li>",
            "<li>Chen S, Zhou Y, Chen Y, Gu J. (2018) fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34(17), i884-i890. doi: 10.1093/bioinformatics/bty560</li>",
            "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047-3048. doi: /10.1093/bioinformatics/btw354.</li>",
            "<li>Gupta NT, Vander Heiden JA, Uduman M, Gadala-Maria D, Yaari G, Kleinstein SH. (2015) Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data. Bioinformatics, 31(20), 3356-3358. doi: 10.1093/bioinformatics/btv359.</li>",
            "<li>Gupta NT, Adams K, Briggs A, Timberlake S, Vigneault F, Kleinstein S (2017). Hierarchical clustering can identify B cell clones with high confidence in Ig repertoire sequencing data. The Journal of Immunology, 2489-2499.</li>",
            "<li>Hoehn KB, Van der Heiden JA, Zhou JQ, Lunter, G, Pybus, OG, & Kleinstein SH. (2019) Repertoire-wide phylogenetic models of B cell molecular evolution reveal evolutionary signatures of aging and vaccination. PNAS, 116(45) 22664-22672. https://www.pnas.org/doi/10.1073/pnas.1906020116</li>",
            "<li>Hoehn K, Pybus O, Kleinstein S (2022). Phylogenetic analysis of migration, differentiation, and class switching in B cells. PLoS Computational Biology. https://doi.org/10.1371/journal.pcbi.1009885.</li>",
            "<li>Nouri N, Kleinstein S (2018). A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data. Bioinformatics, i341-i349.</li>",
            "<li>Stern JN, Yaari G, Vander Heiden JA, Church G, Donahue WF, Hintzen RQ, ... O'Connor, K.C. . (2014) B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes. Sci Transl Med, 6(248), 248ra107. doi: 10.1126/scitranslmed.aaa3822.</li>",
            "<li>Vander Heiden, J. A., Yaari, G., Uduman, M., Stern, J. N. H., O'Connor, K. C., Hafler, D. A., … Kleinstein, S. H. (2014). pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires. Bioinformatics, 30(13), 1930–1932.</li>",
            "<li>Ye J, Ma N, Madden TL, Ostell JM. (2013). IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692102/.</li>"

        ].join(' ').trim()

    return reference_text
}

def methodsDescriptionText(mqc_methods_yaml) {
    // Convert  to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file
    def meta = [:]
    meta.workflow = workflow.toMap()
    meta["manifest_map"] = workflow.manifest.toMap()

    // Pipeline DOI
    if (meta.manifest_map.doi) {
        // Using a loop to handle multiple DOIs
        // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
        // Removing ` ` since the manifest.doi is a string and not a proper list
        def temp_doi_ref = ""
        String[] manifest_doi = meta.manifest_map.doi.tokenize(",")
        for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref.replace("https://doi.org/", "").replace(" ", "")}\'>${doi_ref.replace("https://doi.org/", "").replace(" ", "")}</a>), "
        meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2)
    } else meta["doi_text"] = ""
    meta["nodoi_text"] = meta.manifest_map.doi ? "" : "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"

    // Tool references
    meta["tool_citations"] = ""
    meta["tool_bibliography"] = ""

    // Tool citations
    meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
    meta["tool_bibliography"] = toolBibliographyText()


    def methods_text = mqc_methods_yaml.text

    def engine =  new groovy.text.SimpleTemplateEngine()
    def description_html = engine.createTemplate(methods_text).make(meta)

    return description_html.toString()
}
