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main.nf
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main.nf
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#!/usr/bin/env nextflow
/*
========================================================================================
fmaguire/arete
========================================================================================
Github : https://github.com/fmaguire/arete
----------------------------------------------------------------------------------------
*/
nextflow.enable.dsl = 2
/*
========================================================================================
GENOME PARAMETER VALUES
========================================================================================
*/
//params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
/*
========================================================================================
VALIDATE & PRINT PARAMETER SUMMARY
========================================================================================
*/
// TODO new function to validate our params
WorkflowArete.initialise(workflow, params, log)
/*
========================================================================================
NAMED WORKFLOW FOR PIPELINE
========================================================================================
*/
include { ARETE } from './workflows/arete'
include { ASSEMBLY } from './workflows/arete'
include { ANNOTATION } from './workflows/arete'
include { PHYLO } from './workflows/arete'
include { QUALITYCHECK } from './workflows/arete'
include { POPPUNK } from './workflows/arete'
include { RUN_RSPR } from './workflows/arete'
include { RUN_EVOLCCM } from './workflows/arete'
include { RUN_RECOMBINATION } from './workflows/arete'
include { RUN_GENE_ORDER } from './workflows/arete'
//
// WORKFLOW: Run main nf-core/arete analysis pipeline
//
/*
workflow NFCORE_ARETE {
ARETE ()
}
*/
workflow assembly{
ASSEMBLY ()
}
workflow annotation {
ANNOTATION ()
}
workflow phylogenomics {
PHYLO ()
}
workflow assembly_qc {
QUALITYCHECK()
}
workflow poppunk {
POPPUNK()
}
workflow rspr {
RUN_RSPR()
}
workflow evolccm {
RUN_EVOLCCM()
}
workflow recombination {
RUN_RECOMBINATION()
}
workflow gene_order {
RUN_GENE_ORDER()
}
/*
========================================================================================
RUN ALL WORKFLOWS
========================================================================================
*/
//
// WORKFLOW: Execute a single named workflow for the pipeline
// See: https://github.com/nf-core/rnaseq/issues/619
//
workflow {
ARETE ()
}
/*
========================================================================================
THE END
========================================================================================
*/