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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
========================================================================================
*/
if (!params.fasta) {
params.bowtie2 = WorkflowMain.getGenomeAttribute(params, 'bowtie2')
} else {
params.bowtie2 = null
}
params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
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.spikein_fasta) {
params.spikein_bowtie2 = WorkflowMain.getGenomeAttribute(params, 'bowtie2')
} else {
params.spikein_bowtie2 = null
}
params.spikein_fasta = WorkflowMain.getGenomeAttributeSpikeIn(params, 'fasta')
/*
========================================================================================
VALIDATE & PRINT PARAMETER SUMMARY
========================================================================================
*/
WorkflowMain.initialise(workflow, params, log)
/*
========================================================================================
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
========================================================================================
*/