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main.nf
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main.nf
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#!/usr/bin/env nextflow
/*
========================================================================================
cidgoh_qc
========================================================================================
Github : https://github.com/cidgoh/cidgoh_qc
Website: https://cidgoh.ca/
----------------------------------------------------------------------------------------
*/
nextflow.enable.dsl = 2
/*
========================================================================================
GENOME PARAMETER VALUES
========================================================================================
*/
params.fasta = WorkflowMainQC.getGenomeAttribute(params, 'fasta')
/*
========================================================================================
VALIDATE & PRINT PARAMETER SUMMARY
========================================================================================
*/
WorkflowMainQC.initialise(workflow, params, log)
/*
========================================================================================
NAMED WORKFLOW FOR PIPELINE
========================================================================================
*/
if (params.platform == 'illumina') {
include { ILLUMINA } from './workflows/illumina'
} else if (params.platform == 'nanopore') {
include { NANOPORE } from './workflows/nanopore'
}
//
// WORKFLOW: Run main QC analysis pipeline
//
workflow CIDGOH_QC {
//
// WORKFLOW: QC analysis for Illumina data
//
if (params.platform == 'illumina') {
ILLUMINA ()
//
// WORKFLOW: QC analysis for Nanopore data
//
} else if (params.platform == 'nanopore') {
NANOPORE ()
}
}
/*
========================================================================================
RUN ALL WORKFLOWS
========================================================================================
*/
workflow {
CIDGOH_QC ()
}
/*
========================================================================================
THE END
========================================================================================
*/