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main.nf
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main.nf
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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/cutandrun
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/nf-core/cutandrun
Website: https://nf-co.re/cutandrun
Slack : https://nfcore.slack.com/channels/cutandrun
----------------------------------------------------------------------------------------
*/
nextflow.enable.dsl = 2
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GENOME PARAMETER VALUES
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
params.bowtie2 = WorkflowMain.getGenomeAttribute(params, 'bowtie2')
params.gtf = WorkflowMain.getGenomeAttribute(params, 'gtf')
params.gene_bed = WorkflowMain.getGenomeAttribute(params, 'bed12')
params.blacklist = WorkflowMain.getGenomeAttribute(params, 'blacklist')
/*
========================================================================================
SPIKEIN GENOME PARAMETER VALUES
========================================================================================
*/
if(params.normalisation_mode == "Spikein") {
params.spikein_fasta = WorkflowMain.getGenomeAttributeSpikeIn(params, 'fasta')
params.spikein_bowtie2 = WorkflowMain.getGenomeAttributeSpikeIn(params, 'bowtie2')
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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, args)
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAMED WORKFLOW FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { CUTANDRUN } from './workflows/cutandrun'
workflow NFCORE_CUTANDRUN {
/*
* WORKFLOW: Run main nf-core/cutandrun analysis pipeline
*/
CUTANDRUN ()
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN ALL WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
/*
* WORKFLOW: Execute a single named workflow for the pipeline
* See: https://github.com/nf-core/rnaseq/issues/619
*/
workflow {
NFCORE_CUTANDRUN ()
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/