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Use target bed files as regions instead of bait intervals for SNV calling in WES samples #636

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merged 6 commits into from
Oct 25, 2024
Merged

Use target bed files as regions instead of bait intervals for SNV calling in WES samples #636

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c9773e4
use target bed instead of bait intervals
ramprasadn Oct 18, 2024
a628d51
add decompress
ramprasadn Oct 22, 2024
cce6cd1
Merge branch 'dev' into targetbedtodeepvariant
ramprasadn Oct 22, 2024
24946a5
Merge branch 'dev' into targetbedtodeepvariant
ramprasadn Oct 22, 2024
45901d8
Update CHANGELOG.md
ramprasadn Oct 22, 2024
3df34f8
Merge branch 'dev' into targetbedtodeepvariant
ramprasadn Oct 22, 2024
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4 changes: 2 additions & 2 deletions subworkflows/local/call_snv.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ workflow CALL_SNV {
ch_dbsnp // channel: [optional] [ val(meta), path(vcf) ]
ch_dbsnp_tbi // channel: [optional] [ val(meta), path(tbi) ]
ch_call_interval // channel: [mandatory] [ path(intervals) ]
ch_bait_intervals // channel: [mandatory] [ path(intervals) ]
ch_target_bed // channel: [mandatory] [ val(meta), path(bed), path(index) ]
ch_ml_model // channel: [mandatory] [ path(model) ]
ch_par_bed // channel: [optional] [ val(meta), path(bed) ]
ch_case_info // channel: [mandatory] [ val(case_info) ]
Expand All @@ -55,7 +55,7 @@ workflow CALL_SNV {
ch_genome_bam_bai,
ch_genome_fasta,
ch_genome_fai,
ch_bait_intervals,
ch_target_bed,
ch_par_bed,
ch_case_info,
ch_foundin_header,
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6 changes: 4 additions & 2 deletions subworkflows/local/variant_calling/call_snv_deepvariant.nf
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Expand Up @@ -7,6 +7,7 @@ include { BCFTOOLS_NORM as SPLIT_MULTIALLELICS_GL } from '../../../modules/nf
include { BCFTOOLS_NORM as REMOVE_DUPLICATES_GL } from '../../../modules/nf-core/bcftools/norm/main'
include { DEEPVARIANT_RUNDEEPVARIANT as DEEPVARIANT } from '../../../modules/nf-core/deepvariant/rundeepvariant/main'
include { GLNEXUS } from '../../../modules/nf-core/glnexus/main'
include { TABIX_BGZIP } from '../../../modules/nf-core/tabix/bgzip/main'
include { TABIX_TABIX as TABIX_GL } from '../../../modules/nf-core/tabix/tabix/main'
include { TABIX_TABIX as TABIX_ANNOTATE } from '../../../modules/nf-core/tabix/tabix/main'
include { ADD_VARCALLER_TO_BED } from '../../../modules/local/add_varcallername_to_bed'
Expand All @@ -16,7 +17,7 @@ workflow CALL_SNV_DEEPVARIANT {
ch_bam_bai // channel: [mandatory] [ val(meta), path(bam), path(bai) ]
ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ]
ch_genome_fai // channel: [mandatory] [ val(meta), path(fai) ]
ch_bait_intervals // channel: [mandatory] [ path(intervals) ]
ch_target_bed // channel: [mandatory] [ val(meta), path(bed), path(index) ]
ch_par_bed // channel: [optional] [ val(meta), path(bed) ]
ch_case_info // channel: [mandatory] [ val(case_info) ]
ch_foundin_header // channel: [mandatory] [ path(header) ]
Expand All @@ -26,8 +27,9 @@ workflow CALL_SNV_DEEPVARIANT {
ch_versions = Channel.empty()

if (params.analysis_type.equals("wes")) {
TABIX_BGZIP(ch_target_bed.map{meta, gzbed, index -> return [meta, gzbed]})
ch_bam_bai
.combine (ch_bait_intervals)
.combine (TABIX_BGZIP.out.output.map {meta, bed -> return bed})
.set { ch_deepvar_in }
} else if (params.analysis_type.equals("wgs")) {
ch_bam_bai
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2 changes: 1 addition & 1 deletion workflows/raredisease.nf
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Expand Up @@ -517,7 +517,7 @@ workflow RAREDISEASE {
ch_dbsnp,
ch_dbsnp_tbi,
ch_call_interval,
ch_bait_intervals,
ch_target_bed,
ch_ml_model,
ch_par_bed,
ch_case_info,
Expand Down
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