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main.nf
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main.nf
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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
plant-food-research-open/assemblyqc
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/plant-food-research-open/assemblyqc
----------------------------------------------------------------------------------------
*/
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { ASSEMBLYQC } from './workflows/assemblyqc'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_assemblyqc_pipeline'
include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_assemblyqc_pipeline'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAMED WORKFLOWS FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
//
// WORKFLOW: Run main analysis pipeline depending on type of input
//
workflow PLANTFOODRESEARCHOPEN_ASSEMBLYQC {
take:
ch_input
ch_hic_reads
ch_xref_assembly
ch_reads
ch_maternal_reads
ch_paternal_reads
ch_params_as_json
ch_summary_params_as_json
main:
//
// WORKFLOW: Run pipeline
//
ASSEMBLYQC (
ch_input,
ch_hic_reads,
ch_xref_assembly,
ch_reads,
ch_maternal_reads,
ch_paternal_reads,
ch_params_as_json,
ch_summary_params_as_json
)
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN MAIN WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
workflow {
main:
//
// SUBWORKFLOW: Run initialisation tasks
//
PIPELINE_INITIALISATION (
params.version,
params.monochrome_logs,
args,
params.outdir,
params.input
)
//
// WORKFLOW: Run main workflow
//
PLANTFOODRESEARCHOPEN_ASSEMBLYQC (
PIPELINE_INITIALISATION.out.input,
PIPELINE_INITIALISATION.out.hic_reads,
PIPELINE_INITIALISATION.out.xref_assembly,
PIPELINE_INITIALISATION.out.reads,
PIPELINE_INITIALISATION.out.maternal_reads,
PIPELINE_INITIALISATION.out.paternal_reads,
PIPELINE_INITIALISATION.out.params_as_json,
PIPELINE_INITIALISATION.out.summary_params_as_json
)
//
// SUBWORKFLOW: Run completion tasks
//
PIPELINE_COMPLETION (
params.email,
params.email_on_fail,
params.plaintext_email,
params.outdir,
params.monochrome_logs,
params.hook_url,
)
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/