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//
// PAIRED VARIANT CALLING
//
include { GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING } from '../../subworkflows/nf-core/gatk4/tumor_normal_somatic_variant_calling/main'
include { MSISENSORPRO_MSI_SOMATIC } from '../../modules/nf-core/modules/msisensorpro/msi_somatic/main'
include { RUN_CONTROLFREEC_SOMATIC } from '../nf-core/variantcalling/controlfreec/somatic/main.nf'
include { RUN_FREEBAYES as RUN_FREEBAYES_SOMATIC } from '../nf-core/variantcalling/freebayes/main.nf'
include { RUN_MANTA_SOMATIC } from '../nf-core/variantcalling/manta/somatic/main.nf'
include { RUN_STRELKA_SOMATIC } from '../nf-core/variantcalling/strelka/somatic/main.nf'
include { RUN_CNVKIT_SOMATIC } from '../nf-core/variantcalling/cnvkit/somatic/main.nf'
include { RUN_MPILEUP as RUN_MPILEUP_NORMAL } from '../nf-core/variantcalling/mpileup/main'
include { RUN_MPILEUP as RUN_MPILEUP_TUMOR } from '../nf-core/variantcalling/mpileup/main'
include { RUN_ASCAT_SOMATIC } from '../nf-core/variantcalling/ascat/main'
include { RUN_TIDDIT as RUN_TIDDIT_NORMAL } from '../nf-core/variantcalling/tiddit/main.nf'
include { RUN_TIDDIT as RUN_TIDDIT_TUMOR } from '../nf-core/variantcalling/tiddit/main.nf'
include { SVDB_MERGE } from '../../modules/nf-core/modules/svdb/merge/main.nf'
workflow PAIR_VARIANT_CALLING {
take:
tools // Mandatory, list of tools to apply
cram_pair // channel: [mandatory] cram
bwa // channel: [optional] bwa
chr_files
dbsnp // channel: [mandatory] dbsnp
dbsnp_tbi // channel: [mandatory] dbsnp_tbi
dict // channel: [mandatory] dict
fasta // channel: [mandatory] fasta
fasta_fai // channel: [mandatory] fasta_fai
germline_resource // channel: [optional] germline_resource
germline_resource_tbi // channel: [optional] germline_resource_tbi
intervals // channel: [mandatory] intervals/target regions
intervals_bed_gz_tbi // channel: [mandatory] intervals/target regions index zipped and indexed
intervals_bed_combined // channel: [mandatory] intervals/target regions in one file unzipped
mappability
msisensorpro_scan // channel: [optional] msisensorpro_scan
panel_of_normals // channel: [optional] panel_of_normals
panel_of_normals_tbi // channel: [optional] panel_of_normals_tbi
allele_files // channel: [optional] ascat allele files
loci_files // channel: [optional] ascat loci files
gc_file // channel: [optional] ascat gc content file
rt_file // channel: [optional] ascat rt file
main:
ch_versions = Channel.empty()
//TODO: Temporary until the if's can be removed and printing to terminal is prevented with "when" in the modules.config
freebayes_vcf = Channel.empty()
manta_vcf = Channel.empty()
strelka_vcf = Channel.empty()
msisensorpro_output = Channel.empty()
mutect2_vcf = Channel.empty()
tiddit_vcf = Channel.empty()
// Remap channel with intervals
cram_pair_intervals = cram_pair.combine(intervals)
.map{ meta, normal_cram, normal_crai, tumor_cram, tumor_crai, intervals, num_intervals ->
//If no interval file provided (0) then add empty list
intervals_new = num_intervals == 0 ? [] : intervals
[[patient:meta.patient, normal_id:meta.normal_id, tumor_id:meta.tumor_id, sex:meta.sex, id: meta.tumor_id + "_vs_" + meta.normal_id, num_intervals:num_intervals],
normal_cram, normal_crai, tumor_cram, tumor_crai, intervals_new]
}
// Remap channel with gzipped intervals + indexes
cram_pair_intervals_gz_tbi = cram_pair.combine(intervals_bed_gz_tbi)
.map{ meta, normal_cram, normal_crai, tumor_cram, tumor_crai, bed_tbi, num_intervals ->
//If no interval file provided (0) then add empty list
bed_new = num_intervals == 0 ? [] : bed_tbi[0]
tbi_new = num_intervals == 0 ? [] : bed_tbi[1]
[[patient:meta.patient, normal_id:meta.normal_id, tumor_id:meta.tumor_id, sex:meta.sex, id: meta.tumor_id + "_vs_" + meta.normal_id, num_intervals:num_intervals],
normal_cram, normal_crai, tumor_cram, tumor_crai, bed_new, tbi_new]
}
if (tools.contains('ascat')){
RUN_ASCAT_SOMATIC( cram_pair,
allele_files,
loci_files,
intervals_bed_combined,
fasta,
gc_file,
rt_file)
ch_versions = ch_versions.mix(RUN_ASCAT_SOMATIC.out.versions)
}
if (tools.contains('controlfreec')){
cram_normal_intervals_no_index = cram_pair_intervals
.map {meta, normal_cram, normal_crai, tumor_cram, tumor_crai, intervals ->
[meta, normal_cram, intervals]
}
cram_tumor_intervals_no_index = cram_pair_intervals
.map {meta, normal_cram, normal_crai, tumor_cram, tumor_crai, intervals ->
[meta, tumor_cram, intervals]
}
RUN_MPILEUP_NORMAL(cram_normal_intervals_no_index, fasta)
RUN_MPILEUP_TUMOR(cram_tumor_intervals_no_index, fasta)
mpileup_normal = RUN_MPILEUP_NORMAL.out.mpileup
mpileup_tumor = RUN_MPILEUP_TUMOR.out.mpileup
controlfreec_input = mpileup_normal.cross(mpileup_tumor)
.map{ normal, tumor ->
[normal[0], normal[1], tumor[1], [], [], [], []]
}
RUN_CONTROLFREEC_SOMATIC(controlfreec_input,
fasta,
fasta_fai,
dbsnp,
dbsnp_tbi,
chr_files,
mappability,
intervals_bed_combined)
ch_versions = ch_versions.mix(RUN_MPILEUP_NORMAL.out.versions)
ch_versions = ch_versions.mix(RUN_MPILEUP_TUMOR.out.versions)
ch_versions = ch_versions.mix(RUN_CONTROLFREEC_SOMATIC.out.versions)
}
if (tools.contains('cnvkit')){
cram_pair_cnvkit_somatic = cram_pair
.map{meta, normal_cram, normal_crai, tumor_cram, tumor_crai ->
[meta, tumor_cram, normal_cram]
}
RUN_CNVKIT_SOMATIC( cram_pair_cnvkit_somatic,
fasta,
fasta_fai,
intervals_bed_combined,
[])
}
if (tools.contains('freebayes')){
RUN_FREEBAYES_SOMATIC(cram_pair_intervals, dict, fasta, fasta_fai)
freebayes_vcf = RUN_FREEBAYES_SOMATIC.out.freebayes_vcf
ch_versions = ch_versions.mix(RUN_FREEBAYES_SOMATIC.out.versions)
}
if (tools.contains('manta')) {
RUN_MANTA_SOMATIC( cram_pair_intervals_gz_tbi,
dict,
fasta,
fasta_fai)
manta_vcf = RUN_MANTA_SOMATIC.out.manta_vcf
manta_candidate_small_indels_vcf = RUN_MANTA_SOMATIC.out.manta_candidate_small_indels_vcf
manta_candidate_small_indels_vcf_tbi = RUN_MANTA_SOMATIC.out.manta_candidate_small_indels_vcf_tbi
ch_versions = ch_versions.mix(RUN_MANTA_SOMATIC.out.versions)
}
if (tools.contains('strelka')) {
if (tools.contains('manta')) {
cram_pair_strelka = cram_pair.join(manta_candidate_small_indels_vcf)
.join(manta_candidate_small_indels_vcf_tbi)
.combine(intervals_bed_gz_tbi)
.map{
meta, normal_cram, normal_crai, tumor_cram, tumor_crai, vcf, vcf_tbi, bed_tbi, num_intervals ->
//If no interval file provided (0) then add empty list
bed_new = num_intervals == 0 ? [] : bed_tbi[0]
tbi_new = num_intervals == 0 ? [] : bed_tbi[1]
[[patient:meta.patient, normal_id:meta.normal_id, tumor_id:meta.tumor_id, sex:meta.sex, id:meta.tumor_id + "_vs_" + meta.normal_id, num_intervals:num_intervals],
normal_cram, normal_crai, tumor_cram, tumor_crai, vcf, vcf_tbi, bed_new, tbi_new]
}
} else {
cram_pair_strelka = cram_pair_intervals_gz_tbi.map{
meta, normal_cram, normal_crai, tumor_cram, tumor_crai, bed, tbi ->
[meta, normal_cram, normal_crai, tumor_cram, tumor_crai, [], [], bed, tbi]
}
}
RUN_STRELKA_SOMATIC(cram_pair_strelka,
dict,
fasta,
fasta_fai)
strelka_vcf = Channel.empty().mix(RUN_STRELKA_SOMATIC.out.strelka_vcf)
ch_versions = ch_versions.mix(RUN_STRELKA_SOMATIC.out.versions)
}
if (tools.contains('msisensorpro')) {
cram_pair_msisensor = cram_pair.combine(intervals_bed_combined)
MSISENSORPRO_MSI_SOMATIC(cram_pair_msisensor, fasta, msisensorpro_scan)
ch_versions = ch_versions.mix(MSISENSORPRO_MSI_SOMATIC.out.versions)
msisensorpro_output = msisensorpro_output.mix(MSISENSORPRO_MSI_SOMATIC.out.output_report)
}
if (tools.contains('mutect2')) {
cram_pair_mutect2 = cram_pair_intervals.map{ meta, normal_cram, normal_crai, tumor_cram, tumor_crai, intervals ->
[meta, [normal_cram, tumor_cram], [normal_crai, tumor_crai], intervals]
}
GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING(
cram_pair_mutect2,
fasta,
fasta_fai,
dict,
germline_resource,
germline_resource_tbi,
panel_of_normals,
panel_of_normals_tbi)
mutect2_vcf = GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING.out.filtered_vcf
ch_versions = ch_versions.mix(GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING.out.versions)
}
//TIDDIT
if (tools.contains('tiddit')){
cram_normal = cram_pair.map{meta, normal_cram, normal_crai, tumor_cram, tumor_crai ->
[meta, normal_cram, normal_crai]
}
cram_tumor = cram_pair.map{meta, normal_cram, normal_crai, tumor_cram, tumor_crai ->
[meta, tumor_cram, tumor_crai]
}
RUN_TIDDIT_NORMAL(cram_normal, fasta, bwa)
RUN_TIDDIT_TUMOR(cram_tumor, fasta, bwa)
SVDB_MERGE(RUN_TIDDIT_NORMAL.out.tiddit_vcf.join(RUN_TIDDIT_TUMOR.out.tiddit_vcf)
.map{meta, vcf_normal, vcf_tumor ->
[meta, [vcf_normal, vcf_tumor]]
}, false)
tiddit_vcf = SVDB_MERGE.out.vcf
ch_versions = ch_versions.mix(RUN_TIDDIT_NORMAL.out.versions)
ch_versions = ch_versions.mix(RUN_TIDDIT_TUMOR.out.versions)
ch_versions = ch_versions.mix(SVDB_MERGE.out.versions)
}
emit:
freebayes_vcf
manta_vcf
msisensorpro_output
mutect2_vcf
strelka_vcf
tiddit_vcf
versions = ch_versions
}