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main.nf
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main.nf
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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/phageannotator
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/nf-core/phageannotator
Website: https://nf-co.re/phageannotator
Slack : https://nfcore.slack.com/channels/phageannotator
----------------------------------------------------------------------------------------
*/
nextflow.enable.dsl = 2
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
//
// PLUGIN: Installed from nextflow plugins
//
include { paramsSummaryMap } from 'plugin/nf-validation'
//
// MODULE
//
include { MULTIQC } from './modules/nf-core/multiqc/main'
include { FASTQC } from './modules/nf-core/fastqc/main'
//
// SUBWORKFLOW
//
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_phageannotator_pipeline'
include { paramsSummaryMultiqc } from './subworkflows/nf-core/utils_nfcore_pipeline'
include { softwareVersionsToYAML } from './subworkflows/nf-core/utils_nfcore_pipeline'
include { methodsDescriptionText } from './subworkflows/local/utils_nfcore_phageannotator_pipeline'
include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_phageannotator_pipeline'
//
// WORKFLOW
//
include { PHAGEANNOTATOR } from './workflows/phageannotator/main'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAMED WORKFLOW FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
//
// WORKFLOW: Run main analysis pipeline depending on type of input
//
workflow NFCORE_PHAGEANNOTATOR {
take:
samplesheet // channel: samplesheet read in from --input
main:
ch_fastq_gz = samplesheet.map { meta, fastq, fasta -> return [ meta, fastq ] }
ch_fasta_gz = samplesheet.map { meta, fastq, fasta -> return [ meta, fasta ] }
//
// WORKFLOW: Run pipeline
//
PHAGEANNOTATOR (
ch_fastq_gz,
ch_fasta_gz
)
emit:
versions = PHAGEANNOTATOR.out.versions
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN MAIN WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
workflow {
main:
ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty()
//
// SUBWORKFLOW: Run initialisation tasks
//
PIPELINE_INITIALISATION (
params.version,
params.help,
params.validate_params,
params.monochrome_logs,
args,
params.outdir,
params.input
)
//
// MODULE: Run FastQC
//
FASTQC (
PIPELINE_INITIALISATION.out.samplesheet.map { meta, fastq, fasta -> return [ meta, fastq ] }
)
ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]})
ch_versions = ch_versions.mix(FASTQC.out.versions.first())
//
// WORKFLOW: Run main workflow
//
NFCORE_PHAGEANNOTATOR (
PIPELINE_INITIALISATION.out.samplesheet
)
//
// Collate and save software versions
//
softwareVersionsToYAML(NFCORE_PHAGEANNOTATOR.out.versions)
.collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true)
.set { ch_collated_versions }
//
// MODULE: MultiQC
//
ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false))
MULTIQC (
ch_multiqc_files.collect(),
ch_multiqc_config.toList(),
ch_multiqc_custom_config.toList(),
ch_multiqc_logo.toList()
)
ch_multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
//
// SUBWORKFLOW: Run completion tasks
//
PIPELINE_COMPLETION (
params.email,
params.email_on_fail,
params.plaintext_email,
params.outdir,
params.monochrome_logs,
params.hook_url,
ch_multiqc_report
)
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/