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main.nf
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main.nf
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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/tbanalyzer
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/nf-core/tbanalyzer
Website: https://nf-co.re/tbanalyzer
Slack : https://nfcore.slack.com/channels/tbanalyzer
----------------------------------------------------------------------------------------
*/
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { TBANALYZER } from './workflows/tbanalyzer'
include { MTBSEQ_NF } from './workflows/mtbseqnf'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_tbanalyzer_pipeline'
include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_tbanalyzer_pipeline'
include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_tbanalyzer_pipeline'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GENOME PARAMETER VALUES
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
// TODO nf-core: Remove this line if you don't need a FASTA file
// This is an example of how to use getGenomeAttribute() to fetch parameters
// from igenomes.config using `--genome`
params.fasta = getGenomeAttribute('fasta')
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAMED WORKFLOWS FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
//
// WORKFLOW: Run main analysis pipeline depending on type of input
//
workflow NFCORE_TBANALYZER {
take:
samplesheet // channel: samplesheet read in from --input
main:
// SELECT MODE:
// MTBSEQ run mode
if(params.mode == "mtbseq") {
MTBSEQ_NF (
samplesheet
)
multiqc_report = MTBSEQ_NF.out.multiqc_report
}
// WORKFLOW: Run pipeline
//
//TBANALYZER (
// samplesheet
//)
emit:
multiqc_report = multiqc_report // channel: /path/to/multiqc_report.html
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN MAIN WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
workflow {
main:
//
// SUBWORKFLOW: Run initialisation tasks
//
PIPELINE_INITIALISATION (
params.version,
params.validate_params,
params.monochrome_logs,
args,
params.outdir,
params.input
)
//
// WORKFLOW: Run main workflow
//
NFCORE_TBANALYZER (
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_TBANALYZER.out.multiqc_report
)
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/