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main.nf
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main.nf
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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/atacseq
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/nf-core/atacseq
Website: https://nf-co.re/atacseq
Slack : https://nfcore.slack.com/channels/atacseq
----------------------------------------------------------------------------------------
*/
nextflow.enable.dsl = 2
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GENOME PARAMETER VALUES
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
params.bwa_index = WorkflowMain.getGenomeAttribute(params, 'bwa')
params.bowtie2_index = WorkflowMain.getGenomeAttribute(params, 'bowtie2')
params.chromap_index = WorkflowMain.getGenomeAttribute(params, 'chromap')
params.star_index = WorkflowMain.getGenomeAttribute(params, 'star')
params.gtf = WorkflowMain.getGenomeAttribute(params, 'gtf')
params.gff = WorkflowMain.getGenomeAttribute(params, 'gff')
params.gene_bed = WorkflowMain.getGenomeAttribute(params, 'gene_bed')
params.tss_bed = WorkflowMain.getGenomeAttribute(params, 'tss_bed')
params.blacklist = WorkflowMain.getGenomeAttribute(params, 'blacklist')
params.mito_name = WorkflowMain.getGenomeAttribute(params, 'mito_name')
params.macs_gsize = WorkflowMain.getMacsGsize(params)
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 { ATACSEQ } from './workflows/atacseq'
//
// WORKFLOW: Run main nf-core/atacseq analysis pipeline
//
workflow NFCORE_ATACSEQ {
ATACSEQ ()
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN ALL WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
//
// WORKFLOW: Execute a single named workflow for the pipeline
// See: https://github.com/nf-core/rnaseq/issues/619
//
workflow {
NFCORE_ATACSEQ ()
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/