scdownstream/main.nf at dev_ukdri · UKDRI/scdownstream · GitHub

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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    nf-core/scdownstream
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Github : https://github.com/nf-core/scdownstream
    Website: https://nf-co.re/scdownstream
    Slack  : https://nfcore.slack.com/channels/scdownstream
----------------------------------------------------------------------------------------
*/

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

include { SCDOWNSTREAM            } from './workflows/scdownstream'
include { QC_CLUSTER              } from './workflows/qc_clustering'
include { DOWNSTREAM_ANALYSIS     } from './workflows/downstream'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_scdownstream_pipeline'
include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_scdownstream_pipeline'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    NAMED WORKFLOWS FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

//
// WORKFLOW: Run main analysis pipeline depending on type of input
//
workflow NFCORE_SCDOWNSTREAM {

    take:
    samplesheet // channel: samplesheet read in from --input
    ch_base  // value channel: [ val(meta), path(h5ad) ]

    main:

    //
    // WORKFLOW: Run pipeline
    //
    SCDOWNSTREAM (
        samplesheet,
        ch_base
    )
    emit:
    multiqc_report = SCDOWNSTREAM.out.multiqc_report // channel: /path/to/multiqc_report.html
}

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    RUN QC and CLUSTERING WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
workflow qc_clustering {

    main:
    //
    // SUBWORKFLOW: Run initialisation tasks
    //
    PIPELINE_INITIALISATION (
        params.version,
        params.validate_params,
        params.monochrome_logs,
        args,
        params.outdir,
        params.input
    )

    //
    // WORKFLOW: Run main workflow
    //
    QC_CLUSTER (
        PIPELINE_INITIALISATION.out.samplesheet,
        params.base_adata
            ? Channel.value([[id: params.name ? params.name : "qc_clustering" ], file(params.base_adata, checkIfExists: true)])
            : Channel.value([[], []])
    )

    //
    // SUBWORKFLOW: Run completion tasks
    //
    PIPELINE_COMPLETION (
        params.email,
        params.email_on_fail,
        params.plaintext_email,
        params.outdir,
        params.monochrome_logs,
        params.hook_url,
        QC_CLUSTER.out.multiqc_report
    )
}

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    RUN DOWNSTREAM WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
workflow downstream {

    main:
    //
    // SUBWORKFLOW: Run initialisation tasks
    //
    PIPELINE_INITIALISATION (
        params.version,
        params.validate_params,
        params.monochrome_logs,
        args,
        params.outdir,
        params.input
    )

    //
    // WORKFLOW: Run main workflow
    //
    DOWNSTREAM_ANALYSIS (
        PIPELINE_INITIALISATION.out.samplesheet,
        params.base_adata
            ? Channel.value([[id: params.name ? params.name : "downstream" ], file(params.base_adata, checkIfExists: true)])
            : Channel.value([[], []])
    )

}

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    RUN MAIN WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

workflow {

    main:
    //
    // SUBWORKFLOW: Run initialisation tasks
    //
    PIPELINE_INITIALISATION (
        params.version,
        params.validate_params,
        params.monochrome_logs,
        args,
        params.outdir,
        params.input
    )

    //
    // WORKFLOW: Run main workflow
    //
    NFCORE_SCDOWNSTREAM (
        PIPELINE_INITIALISATION.out.samplesheet,
        params.base_adata
            ? Channel.value([[id: "base"], file(params.base_adata, checkIfExists: true)])
            : Channel.value([[], []])
    )

    //
    // SUBWORKFLOW: Run completion tasks
    //
    PIPELINE_COMPLETION (
        params.email,
        params.email_on_fail,
        params.plaintext_email,
        params.outdir,
        params.monochrome_logs,
        params.hook_url,
        NFCORE_SCDOWNSTREAM.out.multiqc_report
    )
}

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/