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main.nf
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main.nf
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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/demultiplex
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/nf-core/demultiplex
Website: https://nf-co.re/demultiplex
Slack : https://nfcore.slack.com/channels/demultiplex
----------------------------------------------------------------------------------------
*/
nextflow.enable.dsl = 2
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { DEMULTIPLEX } from './workflows/demultiplex'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_demultiplex_pipeline'
include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_demultiplex_pipeline'
include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_demultiplex_pipeline'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAMED WORKFLOWS FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
//
// WORKFLOW: Run main analysis pipeline depending on type of input
//
workflow NFCORE_DEMULTIPLEX {
take:
samplesheet // channel: samplesheet read in from --input
main:
//
// WORKFLOW: Run pipeline
//
DEMULTIPLEX (
samplesheet
)
emit:
multiqc_report = DEMULTIPLEX.out.multiqc_report // channel: /path/to/multiqc_report.html
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN MAIN WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
workflow {
main:
//
// SUBWORKFLOW: Run initialisation tasks
//
PIPELINE_INITIALISATION (
params.version,
params.help,
params.validate_params,
params.monochrome_logs,
args,
params.outdir,
params.input
)
// WORKFLOW: Run main workflow
NFCORE_DEMULTIPLEX (
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_DEMULTIPLEX.out.multiqc_report
)
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/