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main.nf
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main.nf
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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mskcc/forte
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/mskcc/forte
----------------------------------------------------------------------------------------
*/
nextflow.enable.dsl = 2
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GENOME PARAMETER VALUES
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
params.gtf = WorkflowMain.getGenomeAttribute(params, 'gtf')
params.starfusion_url = WorkflowMain.getGenomeAttribute(params, 'starfusion_url')
params.refflat = WorkflowMain.getGenomeAttribute(params, 'refflat')
params.baits = WorkflowMain.getGenomeAttribute(params, 'baits')
params.cdna = WorkflowMain.getGenomeAttribute(params, 'cdna')
params.arriba_blacklist = WorkflowMain.getGenomeAttribute(params, 'arriba_blacklist')
params.arriba_known_fusions = WorkflowMain.getGenomeAttribute(params, 'arriba_known_fusions')
params.arriba_protein_domains = WorkflowMain.getGenomeAttribute(params, 'arriba_protein_domains')
params.metafusion_blocklist = WorkflowMain.getGenomeAttribute(params, 'metafusion_blocklist')
params.metafusion_gene_bed = WorkflowMain.getGenomeAttribute(params, 'metafusion_gene_bed')
params.metafusion_gene_info = WorkflowMain.getGenomeAttribute(params, 'metafusion_gene_info')
params.ensembl_version = WorkflowMain.getGenomeAttribute(params, 'ensembl_version')
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
VALIDATE & PRINT PARAMETER SUMMARY
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { validateParameters; paramsHelp } from 'plugin/nf-validation'
// Print help message if needed
if (params.help) {
def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker"
log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs)
System.exit(0)
}
// Validate input parameters
if (params.validate_params) {
validateParameters()
}
WorkflowMain.initialise(workflow, params, log)
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAMED WORKFLOW FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { FORTE } from './workflows/forte'
//
// WORKFLOW: Run main mskcc/forte analysis pipeline
//
workflow MSKCC_FORTE {
FORTE ()
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN ALL WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
//
// WORKFLOW: Execute a single named workflow for the pipeline
// See: https://github.com/nf-core/rnaseq/issues/619
//
workflow {
MSKCC_FORTE ()
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/