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Merge pull request #636 from nf-core/targetbedtodeepvariant
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Use target bed files as regions instead of bait intervals for SNV calling in WES samples
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ramprasadn authored Oct 25, 2024
2 parents 610c023 + 3df34f8 commit 31249da
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Showing 3 changed files with 7 additions and 5 deletions.
4 changes: 2 additions & 2 deletions subworkflows/local/call_snv.nf
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
Original file line number Diff line number Diff line change
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
Original file line number Diff line number Diff line change
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,
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