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

CHANGELOG.md

@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Changed`
 
 - Suffix used to identify unique fastq pairs from "\_T" to "\_LNUMBER" [#638](https://github.com/nf-core/raredisease/pull/638)
+- Change the regions used by deepavariant for WES samples from bait interval files to target bed files [#636](https://github.com/nf-core/raredisease/pull/636)
 - Merge output from germlinecnvcaller [#635](https://github.com/nf-core/raredisease/pull/635)
 - Update tools [#623](https://github.com/nf-core/raredisease/pull/623)
 - Update output file name prefix for upd and chromograph to sample-based [#620](https://github.com/nf-core/raredisease/pull/620)

subworkflows/local/call_snv.nf

@@ -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) ]
@@ -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,

subworkflows/local/variant_calling/call_snv_deepvariant.nf

@@ -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'
@@ -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) ]
@@ -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

workflows/raredisease.nf

@@ -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,