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main.nf
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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/fetchngs
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/nf-core/fetchngs
Website: https://nf-co.re/fetchngs
Slack : https://nfcore.slack.com/channels/fetchngs
----------------------------------------------------------------------------------------
*/
nextflow.enable.dsl = 2
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAMED WORKFLOWS FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
if (params.input_type == 'sra') include { SRA } from './workflows/sra'
if (params.input_type == 'synapse') include { SYNAPSE } from './workflows/synapse'
//
// WORKFLOW: Run main nf-core/fetchngs analysis pipeline depending on type of identifier provided
//
workflow NFCORE_FETCHNGS {
take:
ids // channel: database ids read in from --input
main:
ch_versions = Channel.empty()
//
// WORKFLOW: Download FastQ files for SRA / ENA / GEO / DDBJ ids
//
if (params.input_type == 'sra') {
SRA ( ids )
ch_versions = SRA.out.versions
//
// WORKFLOW: Download FastQ files for Synapse ids
//
} else if (params.input_type == 'synapse') {
SYNAPSE ( ids )
ch_versions = SYNAPSE.out.versions
}
emit:
versions = ch_versions
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN ALL WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { PIPELINE_INITIALISATION } from './subworkflows/local/nf_core_fetchngs_utils'
include { PIPELINE_COMPLETION } from './subworkflows/local/nf_core_fetchngs_utils'
//
// WORKFLOW: Execute a single named workflow for the pipeline
//
workflow {
//
// SUBWORKFLOW: Run initialisation tasks
//
PIPELINE_INITIALISATION ()
//
// WORKFLOW: Run primary workflows for the pipeline
//
NFCORE_FETCHNGS (
PIPELINE_INITIALISATION.out.ids
)
//
// SUBWORKFLOW: Run completion tasks
//
PIPELINE_COMPLETION (
NFCORE_FETCHNGS.out.versions,
params.input_type,
params.email,
params.email_on_fail,
params.hook_url,
PIPELINE_INITIALISATION.out.summary_params
)
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/