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refactor and handles intervals thanks to @FriederikeHanssen
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@maxulysse
maxulysse committed Jul 27, 2023
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97 changes: 52 additions & 45 deletions subworkflows/nf-core/bam_create_som_pon_gatk/main.nf
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// Run GATK mutect2, genomicsdbimport and createsomaticpanelofnormals
//

include { GATK4_MUTECT2 } from '../../../modules/nf-core/gatk4/mutect2/main'
include { GATK4_GENOMICSDBIMPORT } from '../../../modules/nf-core/gatk4/genomicsdbimport/main'
include { GATK4_CREATESOMATICPANELOFNORMALS } from '../../../modules/nf-core/gatk4/createsomaticpanelofnormals/main'
include { GATK4_CREATESOMATICPANELOFNORMALS } from '../modules/nf-core/gatk4/createsomaticpanelofnormals/main'
include { GATK4_GENOMICSDBIMPORT } from '../modules/nf-core/gatk4/genomicsdbimport/main'
include { GATK4_MERGEVCFS } from '../modules/nf-core/gatk4/mergevcfs/main'
include { GATK4_MUTECT2 } from '../modules/nf-core/gatk4/mutect2/main'

workflow BAM_CREATE_SOM_PON_GATK {
take:
ch_mutect2_in // channel: [ val(meta), path(input), path(input_index), path(interval_file) ]
ch_input // channel: [ val(meta), path(input), path(input_index), path(interval_file) ]
ch_fasta // channel: [ val(meta), path(fasta) ]
ch_fai // channel: [ val(meta), path(fai) ]
ch_dict // channel: [ val(meta), path(dict) ]
val_pon_norm // string: name for panel of normals
ch_gendb_intervals // channel: [ path(interval_file) ]
ch_intervals // channel: [ path(interval_file) ]

main:
ch_versions = Channel.empty()
ch_input = ch_mutect2_in

//
// Perform variant calling for each sample using mutect2 module in panel of normals mode.
//
GATK4_MUTECT2 (
ch_input,
ch_fasta,
ch_fai,
ch_dict,
[],
[],
[],
[]
)
ch_versions = ch_versions.mix(GATK4_MUTECT2.out.versions.first())

//
// Convert all sample vcfs into a genomicsdb workspace using genomicsdbimport.
//
ch_vcf = GATK4_MUTECT2.out.vcf.collect{it[1]}.toList()
ch_index = GATK4_MUTECT2.out.tbi.collect{it[1]}.toList()
ch_dict_gendb = ch_dict.map{meta, dict -> return dict}.toList()

ch_gendb_input = Channel.of([id:val_pon_norm])
.combine(ch_vcf)
.combine(ch_index)
.combine(ch_gendb_intervals)
.combine(ch_dict_gendb)
.map{meta, vcf, tbi, interval, dict -> [meta, vcf, tbi, interval, [], dict]}

GATK4_GENOMICSDBIMPORT ( ch_gendb_input, false, false, false )
ch_versions = ch_versions.mix(GATK4_GENOMICSDBIMPORT.out.versions.first())
// Combine input and intervals for spread and gather strategy
ch_input_intervals = ch_input.combine(ch_intervals)
// Move num_intervals to meta map and reorganize channel for MUTECT2_PAIRED module
.map{ meta, input_list, input_index_list, intervals, num_intervals -> [ meta + [ num_intervals:num_intervals ], input_list, input_index_list, intervals ] }

//
//Panel of normals made from genomicsdb workspace using createsomaticpanelofnormals.
//
GATK4_CREATESOMATICPANELOFNORMALS ( GATK4_GENOMICSDBIMPORT.out.genomicsdb, ch_fasta, ch_fai, ch_dict )
GATK4_MUTECT2(ch_input_intervals, ch_fasta, ch_fai, ch_dict, [], [], [], [])

// Figuring out if there is one or more vcf(s) from the same sample
vcf_branch = GATK4_MUTECT2.out.vcf.branch{
// Use meta.num_intervals to asses number of intervals
intervals: it[0].num_intervals > 1
no_intervals: it[0].num_intervals <= 1
}

// Figuring out if there is one or more tbi(s) from the same sample
tbi_branch = GATK4_MUTECT2.out.tbi.branch{
// Use meta.num_intervals to asses number of intervals
intervals: it[0].num_intervals > 1
no_intervals: it[0].num_intervals <= 1
}

vcf_to_merge = vcf_branch.intervals.map{ meta, vcf -> [ groupKey(meta, meta.num_intervals), vcf ] }.groupTuple()

GATK4_MERGEVCFS(vcf_to_merge, ch_dict)

vcf = Channel.empty().mix(GATK4_MERGEVCFS.out.vcf, vcf_branch.no_intervals)
tbi = Channel.empty().mix(GATK4_MERGEVCFS.out.tbi, tbi_branch.no_intervals)

vcf_joint = vcf.map{ meta, vcf -> [[id: 'joint'], vcf]}.groupTuple()
tbi_joint = tbi.map{ meta, tbi -> [[id: 'joint'], tbi]}.groupTuple()

ch_genomicsdb_input = vcf_joint.join(tbi_joint).combine(intervals_test).map{ meta, vcf, tbi, intervals -> [meta, vcf, tbi, intervals, [], [] ]}

GATK4_GENOMICSDBIMPORT(ch_genomicsdb_input, [], [], [])
GATK4_CREATESOMATICPANELOFNORMALS(GATK4_GENOMICSDBIMPORT.out.genomicsdb, ch_fasta, ch_fai, ch_dict)

ch_versions = ch_versions.mix(GATK4_MUTECT2.out.versions.first())
ch_versions = ch_versions.mix(GATK4_MERGEVCFS.out.versions.first())
ch_versions = ch_versions.mix(GATK4_GENOMICSDBIMPORT.out.versions.first())
ch_versions = ch_versions.mix(GATK4_CREATESOMATICPANELOFNORMALS.out.versions.first())

emit:
mutect2_vcf = GATK4_MUTECT2.out.vcf // channel: [ val(meta), path(vcf) ]
mutect2_index = GATK4_MUTECT2.out.tbi // channel: [ val(meta), path(tbi) ]
mutect2_stats = GATK4_MUTECT2.out.stats // channel: [ val(meta), path(stats) ]
genomicsdb = GATK4_GENOMICSDBIMPORT.out.genomicsdb // channel: [ val(meta), path(genomicsdb) ]
pon_vcf = GATK4_CREATESOMATICPANELOFNORMALS.out.vcf // channel: [ val(meta), path(vcf) ]
pon_index = GATK4_CREATESOMATICPANELOFNORMALS.out.tbi // channel: [ val(meta), path(tbi) ]

versions = ch_versions // channel: [ path(versions.yml) ]
vcf = GATK4_MUTECT2.out.vcf // channel: [ val(meta), path(vcf) ]
index = GATK4_MUTECT2.out.tbi // channel: [ val(meta), path(tbi) ]
stats = GATK4_MUTECT2.out.stats // channel: [ val(meta), path(stats) ]
genomicsdb = GATK4_GENOMICSDBIMPORT.out.genomicsdb // channel: [ val(meta), path(genomicsdb) ]
pon_vcf = GATK4_CREATESOMATICPANELOFNORMALS.out.vcf // channel: [ val(meta), path(vcf) ]
pon_index = GATK4_CREATESOMATICPANELOFNORMALS.out.tbi // channel: [ val(meta), path(tbi) ]

versions = ch_versions // channel: [ path(versions.yml) ]
}

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