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main.nf
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#!/usr/bin/env nextflow
nextflow.enable.dsl=2
/*
* Generic multiplatform genome assembly pipeline (MpGAP)
*/
/*
* Include functions
*/
include { helpMessage } from './nf_functions/help.nf'
include { exampleMessage } from './nf_functions/examples.nf'
include { paramsCheck } from './nf_functions/paramsCheck.nf'
include { logMessage } from './nf_functions/logMessages.nf'
/*
* Check parameters
*/
paramsCheck()
params.help = false
if (params.help){
helpMessage()
exit 0
}
params.examples = false
if (params.examples){
exampleMessage()
exit 0
}
/*
Download configuration file, if necessary.
*/
params.get_hybrid_config = false
if (params.get_hybrid_config) {
new File("hybrid.config").write(new URL ("https://github.com/fmalmeida/mpgap/raw/master/configuration_example/hybrid.config").getText())
println ""
println "hybrid.config file saved in working directory"
println "After configuration, run:"
println "nextflow run fmalmeida/mpgap -c ./hybrid.config"
println "Nice code!\n"
exit 0
}
params.get_lreads_config = false
if (params.get_lreads_config) {
new File("lreads-only.config").write(new URL ("https://github.com/fmalmeida/mpgap/raw/master/configuration_example/lreads.config").getText())
println ""
println "lreads.config file saved in working directory"
println "After configuration, run:"
println "nextflow run fmalmeida/mpgap -c ./lreads.config"
println "Nice code!\n"
exit 0
}
params.get_sreads_config = false
if (params.get_sreads_config) {
new File("sreads-only.config").write(new URL ("https://github.com/fmalmeida/mpgap/raw/master/configuration_example/sreads.config").getText())
println ""
println "sreads.config file saved in working directory"
println "After configuration, run:"
println "nextflow run fmalmeida/mpgap -c ./sreads.config"
println "Nice code!\n"
exit 0
}
/*
* Load general parameters and establish defaults
*/
// General
params.outdir = 'output'
params.prefix = ''
params.threads = 4
params.cpus = 2
// Assemblers?
params.skip_flye = false
params.skip_spades = false
params.skip_shovill = false
params.skip_canu = false
params.skip_unicycler = false
params.skip_haslr = false
params.skip_raven = false
params.skip_wtdbg2 = false
params.skip_shasta = false
// Additional parameters for assemblers and quast
params.genomeSize = ''
params.quast_additional_parameters = ''
params.canu_additional_parameters = ''
params.unicycler_additional_parameters = ''
params.flye_additional_parameters = ''
params.spades_additional_parameters = ''
params.shovill_additional_parameters = ''
params.haslr_additional_parameters = ''
params.raven_additional_parameters = ''
params.wtdbg2_additional_parameters = ''
params.wtdbg2_technology = 'ont'
params.shasta_additional_parameters = ''
// Short reads
params.shortreads_paired = ''
params.shortreads_single = ''
// Long reads
params.corrected_lreads = false
params.longreads = ''
params.lr_type = ''
params.medaka_sequencing_model = ''
params.nanopolish_fast5Path = ''
params.nanopolish_max_haplotypes = 1000
params.pacbio_bams = ''
// Hybrid strategy 2
params.strategy_2 = false
params.pilon_memory_limit = 50
/*
* Define log message
*/
logMessage()
/*
* Define custom workflows
*/
// Short reads only
include { sreads_only_nf } from './workflows/short-reads-only.nf'
// Long reads only
include { lreadsonly_nf } from './workflows/long-reads-only.nf'
// Hybrid
include { hybrid_nf } from './workflows/hybrid.nf'
/*
* DEFINE (RUN) MAIN WORKFLOW
*/
workflow {
/*
* Long reads only assembly
*/
if (!params.shortreads_paired && !params.shortreads_single &&
params.longreads && params.lr_type) {
// Giving inputs
lreadsonly_nf(
// Longreads - required
Channel.fromPath(params.longreads),
// Will run Nanopolish?
(params.nanopolish_fast5Path && params.lr_type == 'nanopore') ? Channel.fromPath(params.nanopolish_fast5Path) : Channel.value(''),
(params.nanopolish_fast5Path && params.lr_type == 'nanopore') ? Channel.fromPath(params.nanopolish_fast5Path, type: 'dir') : Channel.value(''),
// Will run gcpp?
(params.pacbio_bams && params.lr_type == 'pacbio') ? Channel.fromPath(params.pacbio_bams).collect() : Channel.value(''),
(params.pacbio_bams && params.lr_type == 'pacbio') ? Channel.fromPath(params.pacbio_bams).count().subscribe { println it } : Channel.value('')
)
}
/*
* Short reads only assembly
*/
if (!params.longreads &&
(params.shortreads_paired || params.shortreads_single)) {
// Giving inputs
sreads_only_nf(
// Have paired end reads?
(params.shortreads_paired) ? Channel.fromFilePairs( params.shortreads_paired, flat: true, size: 2 ) : Channel.value(['', '', '']),
// Have unpaired reads?
(params.shortreads_single) ? Channel.fromPath(params.shortreads_single, hidden: true) : Channel.value('')
)
}
/*
* Hybrid assembly
*/
if (params.longreads && params.lr_type &&
(params.shortreads_paired || params.shortreads_single)) {
// Giving inputs
hybrid_nf(
// Have paired end reads?
(params.shortreads_paired) ? Channel.fromFilePairs( params.shortreads_paired, flat: true, size: 2 ) : Channel.value(['', '', '']),
// Have unpaired reads?
(params.shortreads_single) ? Channel.fromPath(params.shortreads_single, hidden: true) : Channel.value(''),
// Long reads - required
Channel.fromPath(params.longreads),
// Will run Nanopolish?
(params.nanopolish_fast5Path && params.lr_type == 'nanopore') ? Channel.fromPath(params.nanopolish_fast5Path) : Channel.value(''),
(params.nanopolish_fast5Path && params.lr_type == 'nanopore') ? Channel.fromPath(params.nanopolish_fast5Path, type: 'dir') : Channel.value(''),
// Will run Arrow?
(params.pacbio_bams && params.lr_type == 'pacbio') ? Channel.fromPath(params.pacbio_bams).collect() : Channel.value(''),
(params.pacbio_bams && params.lr_type == 'pacbio') ? Channel.fromPath(params.pacbio_bams).count().subscribe { println it } : Channel.value('')
)
}
}
/*
* Completition message
*/
workflow.onComplete {
println "Pipeline completed at: $workflow.complete"
println "Execution status: ${ workflow.success ? 'OK' : 'failed' }"
println "Execution duration: $workflow.duration"
println ""
println "${ workflow.success ? 'I wish you nice results!' : 'Do not give up, we can fix it!' }"
println "${ workflow.success ? 'Thank you for using fmalmeida/mpgap pipeline!' : '' }"
println ""
}