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main.nf
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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/deepmodeloptim
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/nf-core/deepmodeloptim
Website: https://nf-co.re/deepmodeloptim
Slack : https://nfcore.slack.com/channels/deepmodeloptim
----------------------------------------------------------------------------------------
*/
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN ALL WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { DEEPMODELOPTIM } from './workflows/deepmodeloptim'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_deepmodeloptim_pipeline'
include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_deepmodeloptim_pipeline'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAMED WORKFLOWS FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
//
// WORKFLOW: Run main analysis pipeline depending on type of input
//
workflow NFCORE_DEEPMODELOPTIM {
take:
data
data_config
model
model_config
initial_weights
preprocessing_config
genome
main:
//
// WORKFLOW: Run pipeline
//
DEEPMODELOPTIM (
data,
data_config,
model,
model_config,
initial_weights,
preprocessing_config,
genome
)
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN MAIN WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
workflow {
main:
//
// SUBWORKFLOW: Run initialisation tasks
//
PIPELINE_INITIALISATION (
params.version,
params.validate_params,
params.monochrome_logs,
args,
params.outdir,
// and the input files
params.data,
params.data_config,
params.model,
params.model_config,
params.initial_weights,
params.preprocessing_config
)
//
// WORKFLOW: Run main workflow
//
NFCORE_DEEPMODELOPTIM (
PIPELINE_INITIALISATION.out.data,
PIPELINE_INITIALISATION.out.data_config,
PIPELINE_INITIALISATION.out.model,
PIPELINE_INITIALISATION.out.model_config,
PIPELINE_INITIALISATION.out.initial_weights,
PIPELINE_INITIALISATION.out.preprocessing_config,
PIPELINE_INITIALISATION.out.genome
)
//
// 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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/