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main.nf
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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/crisprseq
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/nf-core/crisprseq
Website: https://nf-co.re/crisprseq
Slack : https://nfcore.slack.com/channels/crisprseq
----------------------------------------------------------------------------------------
*/
nextflow.enable.dsl = 2
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_crisprseq_pipeline'
include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_crisprseq_pipeline'
include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_crisprseq_pipeline'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GENOME PARAMETER VALUES
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
params.reference_fasta = params.reference_fasta ?: getGenomeAttribute('fasta')
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAMED WORKFLOWS FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { CRISPRSEQ_TARGETED } from './workflows/crisprseq_targeted'
include { CRISPRSEQ_SCREENING } from './workflows/crisprseq_screening'
//
// WORKFLOW: Run main analysis pipeline depending on type of input
//
workflow NFCORE_CRISPRSEQ {
take:
reads_targeted // channel: fastqc files read in from --input
reads_screening // channel: fastqc files read in from --input
reference // channel: reference sequence read from --input
protospacer // channel: protospacer sequence read from --input
template // channel: template sequence read from --input
main:
//
// WORKFLOW: Run pipeline
//
if ( params.analysis == "targeted" ) {
CRISPRSEQ_TARGETED (
reads_targeted,
reference,
template,
protospacer
)
multiqc_report_ch = CRISPRSEQ_TARGETED.out.multiqc_report
} else if ( params.analysis == "screening" ) {
CRISPRSEQ_SCREENING (reads_screening)
multiqc_report_ch = CRISPRSEQ_SCREENING.out.multiqc_report
}
emit:
multiqc_report = multiqc_report_ch // channel: /path/to/multiqc_report.html
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN MAIN WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
workflow {
main:
//
// SUBWORKFLOW: Run initialisation tasks
//
PIPELINE_INITIALISATION (
params.version,
params.help,
params.validate_params,
params.monochrome_logs,
args,
params.outdir,
params.input
)
//
// WORKFLOW: Run main workflow
//
NFCORE_CRISPRSEQ (
PIPELINE_INITIALISATION.out.reads_targeted,
PIPELINE_INITIALISATION.out.fastqc_screening,
PIPELINE_INITIALISATION.out.reference,
PIPELINE_INITIALISATION.out.protospacer,
PIPELINE_INITIALISATION.out.template
)
//
// SUBWORKFLOW: Run completion tasks
//
PIPELINE_COMPLETION (
params.email,
params.email_on_fail,
params.plaintext_email,
params.outdir,
params.monochrome_logs,
params.hook_url,
NFCORE_CRISPRSEQ.out.multiqc_report
)
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/