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main.nf
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#!/usr/bin/env nextflow
/*
========================================================================================
nf-core/viralrecon
========================================================================================
nf-core/viralrecon Analysis Pipeline.
#### Homepage / Documentation
https://github.com/nf-core/viralrecon
----------------------------------------------------------------------------------------
*/
nextflow.enable.dsl = 2
////////////////////////////////////////////////////
/* -- PRINT HELP -- */
////////////////////////////////////////////////////
log.info Utils.logo(workflow, params.monochrome_logs)
def json_schema = "$projectDir/nextflow_schema.json"
if (params.help) {
def command = "nextflow run nf-core/viralrecon --input samplesheet.csv --genome 'MN908947.3' -profile docker"
log.info NfcoreSchema.paramsHelp(workflow, params, json_schema, command)
log.info Workflow.citation(workflow)
log.info Utils.dashedLine(params.monochrome_logs)
exit 0
}
////////////////////////////////////////////////////
/* -- GENOME PARAMETER VALUES -- */
////////////////////////////////////////////////////
def primer_set = ''
def primer_set_version = 0
if (!params.public_data_ids && params.platform == 'illumina' && params.protocol == 'amplicon') {
primer_set = params.primer_set
primer_set_version = params.primer_set_version
} else if (!params.public_data_ids && params.platform == 'nanopore') {
primer_set = 'artic'
primer_set_version = params.primer_set_version
params.artic_scheme = Workflow.getGenomeAttribute(params, 'scheme', log, primer_set, primer_set_version)
}
params.fasta = Workflow.getGenomeAttribute(params, 'fasta' , log, primer_set, primer_set_version)
params.gff = Workflow.getGenomeAttribute(params, 'gff' , log, primer_set, primer_set_version)
params.bowtie2_index = Workflow.getGenomeAttribute(params, 'bowtie2' , log, primer_set, primer_set_version)
params.primer_bed = Workflow.getGenomeAttribute(params, 'primer_bed', log, primer_set, primer_set_version)
////////////////////////////////////////////////////
/* -- PRINT PARAMETER SUMMARY -- */
////////////////////////////////////////////////////
def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params, json_schema)
log.info NfcoreSchema.paramsSummaryLog(workflow, params, json_schema)
log.info Workflow.citation(workflow)
log.info Utils.dashedLine(params.monochrome_logs)
////////////////////////////////////////////////////
/* -- PARAMETER CHECKS -- */
////////////////////////////////////////////////////
Workflow.validateMainParams(workflow, params, log)
////////////////////////////////////////////////////
/* -- RUN MAIN WORKFLOW -- */
////////////////////////////////////////////////////
workflow {
/*
* WORKFLOW: Get SRA run information for public database ids, download and md5sum check FastQ files, auto-create samplesheet
*/
if (params.public_data_ids) {
include { SRA_DOWNLOAD } from './workflows/sra_download' addParams( summary_params: summary_params )
SRA_DOWNLOAD ()
/*
* WORKFLOW: Variant and de novo assembly analysis for Illumina data
*/
} else if (params.platform == 'illumina') {
include { ILLUMINA } from './workflows/illumina' addParams( summary_params: summary_params )
ILLUMINA ()
/*
* WORKFLOW: Variant analysis for Nanopore data
*/
} else if (params.platform == 'nanopore') {
include { NANOPORE } from './workflows/nanopore' addParams( summary_params: summary_params )
NANOPORE ()
}
}
////////////////////////////////////////////////////
/* -- THE END -- */
////////////////////////////////////////////////////