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main.nf
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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/viralrecon
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/nf-core/viralrecon
Website: https://nf-co.re/viralrecon
Slack : https://nfcore.slack.com/channels/viralrecon
----------------------------------------------------------------------------------------
*/
nextflow.enable.dsl = 2
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GENOME PARAMETER VALUES
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
def primer_set = ''
def primer_set_version = 0
if (params.platform == 'illumina' && params.protocol == 'amplicon') {
primer_set = params.primer_set
primer_set_version = params.primer_set_version
} else if (params.platform == 'nanopore') {
primer_set = 'artic'
primer_set_version = params.primer_set_version
params.artic_scheme = WorkflowMain.getGenomeAttribute(params, 'scheme', log, primer_set, primer_set_version)
}
params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta' , log, primer_set, primer_set_version)
params.gff = WorkflowMain.getGenomeAttribute(params, 'gff' , log, primer_set, primer_set_version)
params.bowtie2_index = WorkflowMain.getGenomeAttribute(params, 'bowtie2' , log, primer_set, primer_set_version)
params.primer_bed = WorkflowMain.getGenomeAttribute(params, 'primer_bed', log, primer_set, primer_set_version)
params.nextclade_dataset = WorkflowMain.getGenomeAttribute(params, 'nextclade_dataset' , log, primer_set, primer_set_version)
params.nextclade_dataset_name = WorkflowMain.getGenomeAttribute(params, 'nextclade_dataset_name' , log, primer_set, primer_set_version)
params.nextclade_dataset_reference = WorkflowMain.getGenomeAttribute(params, 'nextclade_dataset_reference', log, primer_set, primer_set_version)
params.nextclade_dataset_tag = WorkflowMain.getGenomeAttribute(params, 'nextclade_dataset_tag' , log, primer_set, primer_set_version)
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
VALIDATE & PRINT PARAMETER SUMMARY
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
WorkflowMain.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 NFCORE_VIRALRECON {
//
// WORKFLOW: Variant and de novo assembly analysis for Illumina data
//
if (params.platform == 'illumina') {
ILLUMINA ()
//
// WORKFLOW: Variant analysis for Nanopore data
//
} else if (params.platform == 'nanopore') {
NANOPORE ()
}
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN ALL WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
//
// WORKFLOW: Execute a single named workflow for the pipeline
// See: https://github.com/nf-core/rnaseq/issues/619
//
workflow {
NFCORE_VIRALRECON ()
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/