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main.nf
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#!/usr/bin/env nextflow
/*
========================================================================================
nf-core/rnaseq
========================================================================================
nf-core/rnaseq Analysis Pipeline.
#### Homepage / Documentation
https://github.com/nf-core/rnaseq
----------------------------------------------------------------------------------------
*/
nextflow.enable.dsl = 2
////////////////////////////////////////////////////
/* -- PRINT HELP -- */
////////////////////////////////////////////////////
def json_schema = "$projectDir/nextflow_schema.json"
if (params.help) {
def command = "nextflow run nf-core/rnaseq --input samplesheet.csv --genome GRCh37 -profile docker"
log.info Schema.params_help(workflow, params, json_schema, command)
exit 0
}
////////////////////////////////////////////////////
/* -- GENOME PARAMETER VALUES -- */
////////////////////////////////////////////////////
params.fasta = Checks.get_genome_attribute(params, 'fasta')
params.gtf = Checks.get_genome_attribute(params, 'gtf')
params.gff = Checks.get_genome_attribute(params, 'gff')
params.gene_bed = Checks.get_genome_attribute(params, 'bed12')
params.star_index = Checks.get_genome_attribute(params, 'star')
params.hisat2_index = Checks.get_genome_attribute(params, 'hisat2')
params.rsem_index = Checks.get_genome_attribute(params, 'rsem')
params.salmon_index = Checks.get_genome_attribute(params, 'salmon')
////////////////////////////////////////////////////
/* -- 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 genome key exists if provided
Checks.genome_exists(params, log)
////////////////////////////////////////////////////
/* -- RUN MAIN WORKFLOW -- */
////////////////////////////////////////////////////
workflow {
if (params.public_data_ids) {
/*
* SUBWORKFLOW: Get SRA run information for public database ids, download and md5sum check FastQ files, auto-create samplesheet
*/
include { SRA_DOWNLOAD } from './sra_download' addParams( summary_params: summary_params )
SRA_DOWNLOAD ()
} else {
/*
* SUBWORKFLOW: Run main nf-core/rnaseq analysis pipeline
*/
include { RNASEQ } from './rnaseq' addParams( summary_params: summary_params )
RNASEQ ()
}
}
////////////////////////////////////////////////////
/* -- THE END -- */
////////////////////////////////////////////////////