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#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/sarek
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Started March 2016.
Ported to nf-core May 2019.
Ported to DSL 2 July 2020.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/sarek:
An open-source analysis pipeline to detect germline or somatic variants
from whole genome or targeted sequencing
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Github : https:/nf-core/sarek
Website: https://nf-co.re/sarek
Docs : https://nf-co.re/sarek/usage
Slack : https://nfcore.slack.com/channels/sarek
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
nextflow.enable.dsl = 2
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GENOME PARAMETER VALUES
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
params.ascat_alleles = getGenomeAttribute('ascat_alleles')
params.ascat_genome = getGenomeAttribute('ascat_genome')
params.ascat_loci = getGenomeAttribute('ascat_loci')
params.ascat_loci_gc = getGenomeAttribute('ascat_loci_gc')
params.ascat_loci_rt = getGenomeAttribute('ascat_loci_rt')
params.bwa = getGenomeAttribute('bwa')
params.bwamem2 = getGenomeAttribute('bwamem2')
params.cf_chrom_len = getGenomeAttribute('cf_chrom_len')
params.chr_dir = getGenomeAttribute('chr_dir')
params.dbsnp = getGenomeAttribute('dbsnp')
params.dbsnp_tbi = getGenomeAttribute('dbsnp_tbi')
params.dbsnp_vqsr = getGenomeAttribute('dbsnp_vqsr')
params.dict = getGenomeAttribute('dict')
params.dragmap = getGenomeAttribute('dragmap')
params.fasta = getGenomeAttribute('fasta')
params.fasta_fai = getGenomeAttribute('fasta_fai')
params.germline_resource = getGenomeAttribute('germline_resource')
params.germline_resource_tbi = getGenomeAttribute('germline_resource_tbi')
params.intervals = getGenomeAttribute('intervals')
params.known_indels = getGenomeAttribute('known_indels')
params.known_indels_tbi = getGenomeAttribute('known_indels_tbi')
params.known_indels_vqsr = getGenomeAttribute('known_indels_vqsr')
params.known_snps = getGenomeAttribute('known_snps')
params.known_snps_tbi = getGenomeAttribute('known_snps_tbi')
params.known_snps_vqsr = getGenomeAttribute('known_snps_vqsr')
params.mappability = getGenomeAttribute('mappability')
params.ngscheckmate_bed = getGenomeAttribute('ngscheckmate_bed')
params.pon = getGenomeAttribute('pon')
params.pon_tbi = getGenomeAttribute('pon_tbi')
params.sentieon_dnascope_model = getGenomeAttribute('sentieon_dnascope_model')
params.snpeff_db = getGenomeAttribute('snpeff_db')
params.vep_cache_version = getGenomeAttribute('vep_cache_version')
params.vep_genome = getGenomeAttribute('vep_genome')
params.vep_species = getGenomeAttribute('vep_species')
aligner = params.aligner
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
include { SAREK } from './workflows/sarek'
include { ANNOTATION_CACHE_INITIALISATION } from './subworkflows/local/annotation_cache_initialisation'
include { DOWNLOAD_CACHE_SNPEFF_VEP } from './subworkflows/local/download_cache_snpeff_vep'
include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_sarek_pipeline'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_sarek_pipeline'
include { PREPARE_GENOME } from './subworkflows/local/prepare_genome'
include { PREPARE_INTERVALS } from './subworkflows/local/prepare_intervals'
include { PREPARE_REFERENCE_CNVKIT } from './subworkflows/local/prepare_reference_cnvkit'
// Initialize fasta file with meta map:
fasta = params.fasta ? Channel.fromPath(params.fasta).map{ it -> [ [id:it.baseName], it ] }.collect() : Channel.empty()
// Initialize file channels based on params, defined in the params.genomes[params.genome] scope
bcftools_annotations = params.bcftools_annotations ? Channel.fromPath(params.bcftools_annotations).collect() : Channel.empty()
bcftools_header_lines = params.bcftools_header_lines ? Channel.fromPath(params.bcftools_header_lines).collect() : Channel.empty()
cf_chrom_len = params.cf_chrom_len ? Channel.fromPath(params.cf_chrom_len).collect() : []
dbsnp = params.dbsnp ? Channel.fromPath(params.dbsnp).collect() : Channel.value([])
fasta_fai = params.fasta_fai ? Channel.fromPath(params.fasta_fai).collect() : Channel.empty()
germline_resource = params.germline_resource ? Channel.fromPath(params.germline_resource).collect() : Channel.value([]) // Mutect2 does not require a germline resource, so set to optional input
known_indels = params.known_indels ? Channel.fromPath(params.known_indels).collect() : Channel.value([])
known_snps = params.known_snps ? Channel.fromPath(params.known_snps).collect() : Channel.value([])
mappability = params.mappability ? Channel.fromPath(params.mappability).collect() : Channel.value([])
pon = params.pon ? Channel.fromPath(params.pon).collect() : Channel.value([]) // PON is optional for Mutect2 (but highly recommended)
sentieon_dnascope_model = params.sentieon_dnascope_model ? Channel.fromPath(params.sentieon_dnascope_model).collect() : Channel.value([])
// Initialize value channels based on params, defined in the params.genomes[params.genome] scope
ascat_genome = params.ascat_genome ?: Channel.empty()
dbsnp_vqsr = params.dbsnp_vqsr ? Channel.value(params.dbsnp_vqsr) : Channel.empty()
known_indels_vqsr = params.known_indels_vqsr ? Channel.value(params.known_indels_vqsr) : Channel.empty()
known_snps_vqsr = params.known_snps_vqsr ? Channel.value(params.known_snps_vqsr) : Channel.empty()
ngscheckmate_bed = params.ngscheckmate_bed ? Channel.value(params.ngscheckmate_bed) : Channel.empty()
snpeff_db = params.snpeff_db ?: Channel.empty()
vep_cache_version = params.vep_cache_version ?: Channel.empty()
vep_genome = params.vep_genome ?: Channel.empty()
vep_species = params.vep_species ?: Channel.empty()
vep_extra_files = []
if (params.dbnsfp && params.dbnsfp_tbi) {
vep_extra_files.add(file(params.dbnsfp, checkIfExists: true))
vep_extra_files.add(file(params.dbnsfp_tbi, checkIfExists: true))
}
if (params.spliceai_snv && params.spliceai_snv_tbi && params.spliceai_indel && params.spliceai_indel_tbi) {
vep_extra_files.add(file(params.spliceai_indel, checkIfExists: true))
vep_extra_files.add(file(params.spliceai_indel_tbi, checkIfExists: true))
vep_extra_files.add(file(params.spliceai_snv, checkIfExists: true))
vep_extra_files.add(file(params.spliceai_snv_tbi, checkIfExists: true))
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAMED WORKFLOW FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
// WORKFLOW: Run main nf-core/sarek analysis pipeline
workflow NFCORE_SAREK {
take:
samplesheet
main:
versions = Channel.empty()
// build indexes if needed
PREPARE_GENOME(
params.ascat_alleles,
params.ascat_loci,
params.ascat_loci_gc,
params.ascat_loci_rt,
bcftools_annotations,
params.chr_dir,
dbsnp,
fasta,
germline_resource,
known_indels,
known_snps,
pon)
// 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
bwamem2 = params.bwamem2 ? Channel.fromPath(params.bwamem2).map{ it -> [ [id:'bwamem2'], it ] }.collect()
: PREPARE_GENOME.out.bwamem2
dragmap = params.dragmap ? Channel.fromPath(params.dragmap).map{ it -> [ [id:'dragmap'], it ] }.collect()
: PREPARE_GENOME.out.hashtable
// Gather index for mapping given the chosen aligner
index_alignment = (aligner == "bwa-mem" || aligner == "sentieon-bwamem") ? bwa :
aligner == "bwa-mem2" ? bwamem2 :
dragmap
// TODO: add a params for msisensorpro_scan
msisensorpro_scan = PREPARE_GENOME.out.msisensorpro_scan
// For ASCAT, extracted from zip or tar.gz files
allele_files = PREPARE_GENOME.out.allele_files
chr_files = PREPARE_GENOME.out.chr_files
gc_file = PREPARE_GENOME.out.gc_file
loci_files = PREPARE_GENOME.out.loci_files
rt_file = PREPARE_GENOME.out.rt_file
// Tabix indexed vcf files
bcftools_annotations_tbi = params.bcftools_annotations ? params.bcftools_annotations_tbi ? Channel.fromPath(params.bcftools_annotations_tbi).collect() : PREPARE_GENOME.out.bcftools_annotations_tbi : Channel.empty([])
dbsnp_tbi = params.dbsnp ? params.dbsnp_tbi ? Channel.fromPath(params.dbsnp_tbi).collect() : PREPARE_GENOME.out.dbsnp_tbi : Channel.value([])
germline_resource_tbi = params.germline_resource ? params.germline_resource_tbi ? Channel.fromPath(params.germline_resource_tbi).collect() : PREPARE_GENOME.out.germline_resource_tbi : [] //do not change to Channel.value([]), the check for its existence then fails for Getpileupsumamries
known_indels_tbi = params.known_indels ? params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi).collect() : PREPARE_GENOME.out.known_indels_tbi : Channel.value([])
known_snps_tbi = params.known_snps ? params.known_snps_tbi ? Channel.fromPath(params.known_snps_tbi).collect() : PREPARE_GENOME.out.known_snps_tbi : Channel.value([])
pon_tbi = params.pon ? params.pon_tbi ? Channel.fromPath(params.pon_tbi).collect() : PREPARE_GENOME.out.pon_tbi : Channel.value([])
// known_sites is made by grouping both the dbsnp and the known snps/indels resources
// Which can either or both be optional
known_sites_indels = dbsnp.concat(known_indels).collect()
known_sites_indels_tbi = dbsnp_tbi.concat(known_indels_tbi).collect()
known_sites_snps = dbsnp.concat(known_snps).collect()
known_sites_snps_tbi = dbsnp_tbi.concat(known_snps_tbi).collect()
// Build intervals if needed
PREPARE_INTERVALS(fasta_fai, params.intervals, params.no_intervals, params.nucleotides_per_second, params.outdir, params.step)
// Intervals for speed up preprocessing/variant calling by spread/gather
// [interval.bed] all intervals in one file
intervals_bed_combined = params.no_intervals ? Channel.value([]) : PREPARE_INTERVALS.out.intervals_bed_combined
intervals_bed_gz_tbi_combined = params.no_intervals ? Channel.value([]) : PREPARE_INTERVALS.out.intervals_bed_gz_tbi_combined
intervals_bed_combined_for_variant_calling = PREPARE_INTERVALS.out.intervals_bed_combined
// For QC during preprocessing, we don't need any intervals (MOSDEPTH doesn't take them for WGS)
intervals_for_preprocessing = params.wes ?
intervals_bed_combined.map{it -> [ [ id:it.baseName ], it ]}.collect() :
Channel.value([ [ id:'null' ], [] ])
intervals = PREPARE_INTERVALS.out.intervals_bed // [ interval, num_intervals ] multiple interval.bed files, divided by useful intervals for scatter/gather
intervals_bed_gz_tbi = PREPARE_INTERVALS.out.intervals_bed_gz_tbi // [ interval_bed, tbi, num_intervals ] multiple interval.bed.gz/.tbi files, divided by useful intervals for scatter/gather
intervals_and_num_intervals = intervals.map{ interval, num_intervals ->
if ( num_intervals < 1 ) [ [], num_intervals ]
else [ interval, num_intervals ]
}
intervals_bed_gz_tbi_and_num_intervals = intervals_bed_gz_tbi.map{ intervals, num_intervals ->
if ( num_intervals < 1 ) [ [], [], num_intervals ]
else [ intervals[0], intervals[1], num_intervals ]
}
if (params.tools && params.tools.split(',').contains('cnvkit')) {
if (params.cnvkit_reference) {
cnvkit_reference = Channel.fromPath(params.cnvkit_reference).collect()
} else {
PREPARE_REFERENCE_CNVKIT(fasta, intervals_bed_combined)
cnvkit_reference = PREPARE_REFERENCE_CNVKIT.out.cnvkit_reference
versions = versions.mix(PREPARE_REFERENCE_CNVKIT.out.versions)
}
} else {
cnvkit_reference = Channel.value([])
}
// Gather used softwares versions
versions = versions.mix(PREPARE_GENOME.out.versions)
versions = versions.mix(PREPARE_INTERVALS.out.versions)
vep_fasta = (params.vep_include_fasta) ? fasta.map{ fasta -> [ [ id:fasta.baseName ], fasta ] } : [[id: 'null'], []]
// Download cache
if (params.download_cache) {
// Assuming that even if the cache is provided, if the user specify download_cache, sarek will download the cache
ensemblvep_info = Channel.of([ [ id:"${params.vep_cache_version}_${params.vep_genome}" ], params.vep_genome, params.vep_species, params.vep_cache_version ])
snpeff_info = Channel.of([ [ id:"${params.snpeff_db}" ], params.snpeff_db ])
DOWNLOAD_CACHE_SNPEFF_VEP(ensemblvep_info, snpeff_info)
snpeff_cache = DOWNLOAD_CACHE_SNPEFF_VEP.out.snpeff_cache
vep_cache = DOWNLOAD_CACHE_SNPEFF_VEP.out.ensemblvep_cache.map{ meta, cache -> [ cache ] }
versions = versions.mix(DOWNLOAD_CACHE_SNPEFF_VEP.out.versions)
} else {
// Looks for cache information either locally or on the cloud
ANNOTATION_CACHE_INITIALISATION(
(params.snpeff_cache && params.tools && (params.tools.split(',').contains("snpeff") || params.tools.split(',').contains('merge'))),
params.snpeff_cache,
params.snpeff_db,
(params.vep_cache && params.tools && (params.tools.split(',').contains("vep") || params.tools.split(',').contains('merge'))),
params.vep_cache,
params.vep_species,
params.vep_cache_version,
params.vep_genome,
params.vep_custom_args,
"Please refer to https://nf-co.re/sarek/docs/usage/#how-to-customise-snpeff-and-vep-annotation for more information.")
snpeff_cache = ANNOTATION_CACHE_INITIALISATION.out.snpeff_cache
vep_cache = ANNOTATION_CACHE_INITIALISATION.out.ensemblvep_cache
}
//
// WORKFLOW: Run pipeline
//
SAREK(samplesheet,
allele_files,
bcftools_annotations,
bcftools_annotations_tbi,
bcftools_header_lines,
cf_chrom_len,
chr_files,
cnvkit_reference,
dbsnp,
dbsnp_tbi,
dbsnp_vqsr,
dict,
fasta,
fasta_fai,
gc_file,
germline_resource,
germline_resource_tbi,
index_alignment,
intervals_and_num_intervals,
intervals_bed_combined,
intervals_bed_combined_for_variant_calling,
intervals_bed_gz_tbi_and_num_intervals,
intervals_bed_gz_tbi_combined,
intervals_for_preprocessing,
known_indels_vqsr,
known_sites_indels,
known_sites_indels_tbi,
known_sites_snps,
known_sites_snps_tbi,
known_snps_vqsr,
loci_files,
mappability,
msisensorpro_scan,
ngscheckmate_bed,
pon,
pon_tbi,
rt_file,
sentieon_dnascope_model,
snpeff_cache,
vep_cache,
vep_cache_version,
vep_extra_files,
vep_fasta,
vep_genome,
vep_species
)
emit:
multiqc_report = SAREK.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_SAREK(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_SAREK.out.multiqc_report
)
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
FUNCTIONS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
//
// Get attribute from genome config file e.g. fasta
//
def getGenomeAttribute(attribute) {
if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
if (params.genomes[ params.genome ].containsKey(attribute)) {
return params.genomes[ params.genome ][ attribute ]
}
}
return null
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/