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main.nf
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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/fastquorum
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https://github.com/nf-core/fastquorum
Website: https://nf-co.re/fastquorum
Slack : https://nfcore.slack.com/channels/fastquorum
----------------------------------------------------------------------------------------
*/
nextflow.enable.dsl = 2
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GENOME PARAMETER VALUES
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_fastquorum_pipeline'
params.fasta = getGenomeAttribute('fasta')
params.fasta_fai = getGenomeAttribute('fasta_fai')
params.dict = getGenomeAttribute('dict')
params.bwa = getGenomeAttribute('bwa')
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { FASTQUORUM } from './workflows/fastquorum'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_fastquorum_pipeline'
include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_fastquorum_pipeline'
include { PREPARE_GENOME } from './subworkflows/local/prepare_genome'
// Initialize fasta file with meta map:
fasta = params.fasta ? Channel.fromPath(params.fasta).map{ it -> [ [id:it.baseName], it ] }.collect() : Channel.empty()
// Set various consensus calling and filtering parameters if not given
if (params.duplex_seq) {
if (params.groupreadsbyumi_strategy == '') { params.replace("groupreadsbyumi_strategy", 'Paired') }
else if (params.groupreadsbyumi_strategy != 'Paired') {
log.error "config groupreadsbyumi_strategy must be 'Paired' for duplex-sequencing data"
exit 1
}
if (params.call_min_reads == '') { params.replace("call_min_reads", '1 1 0') }
if (!params.filter_min_reads) { params.replace("filter_min_reads", '3 1 1') }
} else {
if (params.groupreadsbyumi_strategy == '') { params.replace("groupreadsbyumi_strategy", 'Adjacency') }
else if (params.groupreadsbyumi_strategy == 'Paired') {
log.error "config groupreadsbyumi_strategy cannot be 'Paired' for non-duplex-sequencing data"
exit 1
}
if (params.call_min_reads == '') { params.replace("call_min_reads", '1') }
if (params.filter_min_reads == '') { params.replace("filter_min_reads", '3') }
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAMED WORKFLOWS FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
//
// WORKFLOW: Run main analysis pipeline depending on type of input
//
workflow NFCORE_FASTQUORUM {
take:
samplesheet // channel: samplesheet read in from --input
main:
versions = Channel.empty()
// WORKFLOW: build indexes if needed
PREPARE_GENOME(fasta)
// Gather built indices or get them from the params
// Built from the fasta file:
dict = params.dict ? Channel.fromPath(params.dict).map{ it -> [ [id:'dict'], it ] }.collect()
: PREPARE_GENOME.out.dict
fasta_fai = params.fasta_fai ? Channel.fromPath(params.fasta_fai).map{ it -> [ [id:'fai'], it ] }.collect()
: PREPARE_GENOME.out.fasta_fai
bwa = params.bwa ? Channel.fromPath(params.bwa).map{ it -> [ [id:'bwa'], it ] }.collect()
: PREPARE_GENOME.out.bwa
//
// WORKFLOW: Run pipeline
//
FASTQUORUM (
params,
samplesheet,
bwa,
dict,
fasta,
fasta_fai
)
emit:
multiqc_report = FASTQUORUM.out.multiqc_report // 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_FASTQUORUM (
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_FASTQUORUM.out.multiqc_report
)
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/