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main.nf
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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/createtaxdb
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/nf-core/createtaxdb
Website: https://nf-co.re/createtaxdb
Slack : https://nfcore.slack.com/channels/createtaxdb
----------------------------------------------------------------------------------------
*/
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { CREATETAXDB } from './workflows/createtaxdb'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_createtaxdb_pipeline'
include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_createtaxdb_pipeline'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN MAIN WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
workflow {
//
// SUBWORKFLOW: Run initialisation tasks
//
PIPELINE_INITIALISATION(
params.version,
params.validate_params,
params.monochrome_logs,
args,
params.outdir,
params.input
)
//
// WORKFLOW: Run main workflow
//
NFCORE_CREATETAXDB(
PIPELINE_INITIALISATION.out.samplesheet
)
//
// SUBWORKFLOW: Run completion tasks
//
PIPELINE_COMPLETION(
params.email,
params.email_on_fail,
params.plaintext_email,
params.outdir,
params.monochrome_logs,
params.hook_url,
NFCORE_CREATETAXDB.out.multiqc_report
)
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAMED WORKFLOWS FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
//
// WORKFLOW: Run main analysis pipeline depending on type of input
//
workflow NFCORE_CREATETAXDB {
take:
samplesheet // channel: samplesheet read in from --input
main:
//
// WORKFLOW: Run pipeline
//
ch_samplesheet = samplesheet
ch_taxonomy_namesdmp = file(params.namesdmp, checkIfExists: true)
ch_taxonomy_nodesdmp = file(params.nodesdmp, checkIfExists: true)
ch_accession2taxid = file(params.accession2taxid, checkIfExists: true)
ch_nucl2taxid = file(params.nucl2taxid, checkIfExists: true)
ch_prot2taxid = file(params.prot2taxid, checkIfExists: true)
ch_malt_mapdb = file(params.malt_mapdb, checkIfExists: true)
CREATETAXDB(
ch_samplesheet,
ch_taxonomy_namesdmp,
ch_taxonomy_nodesdmp,
ch_accession2taxid,
ch_nucl2taxid,
ch_prot2taxid,
ch_malt_mapdb
)
emit:
multiqc_report = CREATETAXDB.out.multiqc_report // channel: /path/to/multiqc_report.html
}