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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 -- */
////////////////////////////////////////////////////
def json_schema = "$projectDir/nextflow_schema.json"
if (params.help) {
def command = "nextflow run nf-core/viralrecon --input samplesheet.csv --genome 'MN908947.3' -profile docker"
log.info Schema.params_help(workflow, params, json_schema, command)
exit 0
}
////////////////////////////////////////////////////
/* -- GENOME PARAMETER VALUES -- */
////////////////////////////////////////////////////
def primer_set = ''
def primer_set_version = 0
if (!params.public_data_ids && params.platform == 'illumina') {
if (params.protocol == 'amplicon') {
primer_set = params.primer_set
primer_set_version = params.primer_set_version
}
} else if (!params.public_data_ids && params.platform == 'nanopore') {
if (params.primer_set != 'artic') {
log.error "Invalid option: --primer_set '${params.primer_set}'. Only --primer_set 'artic' is supported when running the pipeline on Nanopore input data.\n"
System.exit(1)
}
if (!params.primer_set_version) {
log.error "Invalid option: --primer_set_version '${params.primer_set_version}'.\nPlease specify a valid option when using --primer_set '${params.primer_set}'.\n"
System.exit(1)
}
primer_set = params.primer_set
primer_set_version = params.primer_set_version
}
params.fasta = Workflow.get_genome_attribute(params, 'fasta' , log, primer_set, primer_set_version)
params.gff = Workflow.get_genome_attribute(params, 'gff' , log, primer_set, primer_set_version)
params.primer_bed = Workflow.get_genome_attribute(params, 'primer_bed', log, primer_set, primer_set_version)
params.artic_scheme = Workflow.get_genome_attribute(params, 'scheme' , log, primer_set, primer_set_version)
params.bowtie2_index = Workflow.get_genome_attribute(params, 'bowtie2' , log, primer_set, primer_set_version)
////////////////////////////////////////////////////
/* -- PRINT PARAMETER SUMMARY -- */
////////////////////////////////////////////////////
def summary_params = Schema.params_summary_map(workflow, params, json_schema)
log.info Schema.params_summary_log(workflow, params, json_schema)
////////////////////////////////////////////////////
/* -- PARAMETER CHECKS -- */
////////////////////////////////////////////////////
// Check that conda channels are set-up correctly
if (params.enable_conda) {
Checks.check_conda_channels(log)
}
// Check AWS batch settings
Checks.aws_batch(workflow, params)
// Check the hostnames against configured profiles
Checks.hostname(workflow, params, log)
// Check sequencing platform
def platformList = ['illumina', 'nanopore']
if (!params.public_data_ids && !platformList.contains(params.platform)) {
exit 1, "Invalid platform option: ${params.platform}. Valid options: ${platformList.join(', ')}"
}
////////////////////////////////////////////////////
/* -- 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 -- */
////////////////////////////////////////////////////