nascent/main.nf at main · nf-core/nascent · GitHub

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

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

include { NASCENT } from './workflows/nascent'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_nascent_pipeline'
include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_nascent_pipeline'
include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_nascent_pipeline'

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    GENOME PARAMETER VALUES
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

params.fasta = getGenomeAttribute('fasta')
params.gtf = getGenomeAttribute('gtf')
params.gff = getGenomeAttribute('gff')
params.gene_bed = getGenomeAttribute('bed12')
params.bwa_index = getGenomeAttribute('bwa')
params.bwamem2_index = getGenomeAttribute('bwamem2')
params.dragmap = getGenomeAttribute('dragmap')
params.bowtie2_index = getGenomeAttribute('bowtie2')
params.hisat2_index = getGenomeAttribute('hisat2')
params.star_index = null
params.homer_uniqmap = getGenomeAttribute('uniqmap')

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    NAMED WORKFLOWS FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

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

    take:
    samplesheet // channel: samplesheet read in from --input

    main:

    //
    // WORKFLOW: Run pipeline
    //
    NASCENT (
        samplesheet,
        params.fasta,
        params.gtf,
        params.gff,
        params.gene_bed,
        params.bwa_index,
        params.bwamem2_index,
        params.dragmap,
        params.bowtie2_index,
        params.hisat2_index,
        params.star_index,
        params.use_homer_uniqmap ? params.homer_uniqmap : []
    )
    emit:
    multiqc_report = NASCENT.out.multiqc_report // channel: /path/to/multiqc_report.html
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    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_NASCENT (
        PIPELINE_INITIALISATION.out.samplesheet
    )
    //
    // SUBWORKFLOW: Run completion tasks
    //
    PIPELINE_COMPLETION (
        params.email,
        params.email_on_fail,
        params.plaintext_email,
        params.outdir,
        params.monochrome_logs,
        params.hook_url,
        NFCORE_NASCENT.out.multiqc_report
    )
}

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