112 lines
3.2 KiB
Text
112 lines
3.2 KiB
Text
#!/usr/bin/env nextflow
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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nf-core/wartanalysis
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Github : https://github.com/nf-core/wartanalysis
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Website: https://nf-co.re/wartanalysis
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Slack : https://nfcore.slack.com/channels/wartanalysis
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----------------------------------------------------------------------------------------
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*/
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nextflow.enable.dsl = 2
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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*/
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include { WARTANALYSIS } from './workflows/wartanalysis'
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include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_wartanalysis_pipeline'
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include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_wartanalysis_pipeline'
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include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_wartanalysis_pipeline'
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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GENOME PARAMETER VALUES
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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*/
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// TODO nf-core: Remove this line if you don't need a FASTA file
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// This is an example of how to use getGenomeAttribute() to fetch parameters
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// from igenomes.config using `--genome`
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params.fasta = getGenomeAttribute('fasta')
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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NAMED WORKFLOWS FOR PIPELINE
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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*/
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//
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// WORKFLOW: Run main analysis pipeline depending on type of input
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//
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workflow NFCORE_WARTANALYSIS {
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take:
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samplesheet // channel: samplesheet read in from --input
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main:
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//
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// WORKFLOW: Run pipeline
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//
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WARTANALYSIS (
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samplesheet
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)
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emit:
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multiqc_report = WARTANALYSIS.out.multiqc_report // channel: /path/to/multiqc_report.html
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}
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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RUN MAIN WORKFLOW
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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*/
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workflow {
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main:
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//
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// SUBWORKFLOW: Run initialisation tasks
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//
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PIPELINE_INITIALISATION (
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params.version,
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params.help,
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params.validate_params,
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params.monochrome_logs,
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args,
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params.outdir,
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params.input
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)
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//
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// WORKFLOW: Run main workflow
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//
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NFCORE_WARTANALYSIS (
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PIPELINE_INITIALISATION.out.samplesheet
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)
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//
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// SUBWORKFLOW: Run completion tasks
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//
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PIPELINE_COMPLETION (
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params.email,
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params.email_on_fail,
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params.plaintext_email,
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params.outdir,
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params.monochrome_logs,
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params.hook_url,
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NFCORE_WARTANALYSIS.out.multiqc_report
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)
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}
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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THE END
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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*/
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