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main.nf
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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/circrna
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/nf-core/circrna
Website: https://nf-co.re/circrna
Slack : https://nfcore.slack.com/channels/circrna
----------------------------------------------------------------------------------------
*/
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { CIRCRNA } from './workflows/circrna'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_circrna_pipeline'
include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_circrna_pipeline'
include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_circrna_pipeline'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GENOME PARAMETER VALUES
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
params.fasta = getGenomeAttribute('fasta')
params.gtf = getGenomeAttribute('gtf')
params.bwa = getGenomeAttribute('bwa')
params.star = getGenomeAttribute('star')
params.bowtie = getGenomeAttribute('bowtie')
params.bowtie2 = getGenomeAttribute('bowtie2')
params.mature = getGenomeAttribute('mature')
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAMED WORKFLOWS FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
//
// WORKFLOW: Run main analysis pipeline depending on type of input
//
workflow NFCORE_CIRCRNA {
take:
ch_samplesheet
main:
ch_versions = Channel.empty()
//
// WORKFLOW: Run nf-core/circrna workflow
//
ch_fasta = Channel.value([[id: "fasta"], file(params.fasta, checkIfExists:true)])
ch_gtf = Channel.value([[id: "gtf"], file(params.gtf, checkIfExists:true)])
ch_mature = params.mature ? Channel.value([[id: "mature"], file(params.mature, checkIfExists:true)]) : Channel.empty()
ch_phenotype = params.phenotype ? Channel.value([[id: "phenotype"], file(params.phenotype, checkIfExists:true)]) : Channel.empty()
ch_annotation = params.annotation ? Channel.fromSamplesheet("annotation") : Channel.empty()
ch_mirna = params.mature && params.mirna_expression ? Channel.value([[id: "mirna"], file(params.mirna_expression, checkIfExists:true)]) : Channel.empty()
CIRCRNA (
ch_samplesheet,
ch_phenotype,
ch_fasta,
ch_gtf,
ch_mature,
ch_annotation,
ch_versions,
ch_mirna
)
emit:
multiqc_report = CIRCRNA.out.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_CIRCRNA (
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_CIRCRNA.out.multiqc_report
)
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/