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main.nf
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#!/usr/bin/env nextflow
/*
========================================================================================
goodwright/imaps-nf
========================================================================================
Github : https://github.com/goodwright/imaps-nf
Website: https://imaps.goodwright.com/
Slack : https://join.slack.com/t/imapsgroup/shared_invite/zt-r24y3591-Xbhnym2t38u_urU~I0K0lQ
----------------------------------------------------------------------------------------
*/
nextflow.enable.dsl = 2
/*
========================================================================================
GENOME PARAMETER VALUES
========================================================================================
*/
params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
params.gtf = WorkflowMain.getGenomeAttribute(params, 'gtf')
params.gff = WorkflowMain.getGenomeAttribute(params, 'gff')
params.gene_bed = WorkflowMain.getGenomeAttribute(params, 'bed12')
params.star_index = WorkflowMain.getGenomeAttribute(params, 'star')
params.hisat2_index = WorkflowMain.getGenomeAttribute(params, 'hisat2')
params.rsem_index = WorkflowMain.getGenomeAttribute(params, 'rsem')
params.salmon_index = WorkflowMain.getGenomeAttribute(params, 'salmon')
/*
========================================================================================
VALIDATE & PRINT PARAMETER SUMMARY
========================================================================================
*/
WorkflowMain.initialise(workflow, params, log)
/*
========================================================================================
NAMED WORKFLOW FOR PIPELINE
========================================================================================
*/
include { DEMUXANDANALYSE } from './workflows/demuxandanalyse'
//
// WORKFLOW: Run main demultiplex and analyse pipeline
//
workflow IMAPS_DEMUXANDANALYSE {
DEMUXANDANALYSE ()
}
/*
========================================================================================
RUN ALL WORKFLOWS
========================================================================================
*/
//
// WORKFLOW: Execute a single named workflow for the pipeline
// See: https://github.com/nf-core/rnaseq/issues/619
//
workflow {
IMAPS_DEMUXANDANALYSE ()
}
/*
========================================================================================
THE END
========================================================================================
*/