nf-core · asp8200 · Aug 14, 2023 · Aug 14, 2023 · Aug 14, 2023 · Aug 14, 2023
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Installed the nf-core version of the sentieon/readwriter module [#399](https://github.com/nf-core/raredisease/pull/399)
 - Installed the nf-core version of the sentieon/datametrics module [#400](https://github.com/nf-core/raredisease/pull/400)
 - Installed the nf-core version of the sentieon/dedup module. The dedup module also contains a call to Sentieon's LocusCollector [#401](https://github.com/nf-core/raredisease/pull/401)
+- Removing Sentieon-based BQSR. Recent Illumina sequencers tend to provide well-calibrated BQs, so BQSR may not provide much benefit [#402](https://github.com/nf-core/raredisease/pull/402)
 
 ### `Fixed`
 

diff --git a/conf/modules/align_sentieon.config b/conf/modules/align_sentieon.config
@@ -45,7 +45,4 @@ process {
         ]
     }
 
-    withName: '.*ALIGN:ALIGN_SENTIEON:SENTIEON_BQSR' {
-        ext.prefix = { "${meta.id}_bqsr" }
-    }
 }
diff --git a/modules/local/sentieon/bqsr.nf b/modules/local/sentieon/bqsr.nf
diff --git a/subworkflows/local/align.nf b/subworkflows/local/align.nf
@@ -13,8 +13,6 @@ workflow ALIGN {
         ch_genome_fai      // channel: [mandatory] [ val(meta), path(fai) ]
         ch_bwa_index       // channel: [mandatory] [ val(meta), path(index) ]
         ch_bwamem2_index   // channel: [mandatory] [ val(meta), path(index) ]
-        ch_known_dbsnp     // channel: [optional; used by sentieon] [ path(known_dbsnp) ]
-        ch_known_dbsnp_tbi // channel: [optional; used by sentieon] [ path(known_dbsnp_tbi) ]
         val_platform       // string:  [mandatory] illumina or a different technology
 
     main:
@@ -33,8 +31,6 @@ workflow ALIGN {
             ch_genome_fasta,
             ch_genome_fai,
             ch_bwa_index,
-            ch_known_dbsnp,
-            ch_known_dbsnp_tbi,
             val_platform
         )
 

diff --git a/subworkflows/local/alignment/align_sentieon.nf b/subworkflows/local/alignment/align_sentieon.nf
@@ -5,23 +5,17 @@
 include { SENTIEON_BWAMEM         } from '../../../modules/nf-core/sentieon/bwamem/main'
 include { SENTIEON_DATAMETRICS    } from '../../../modules/nf-core/sentieon/datametrics/main'
 include { SENTIEON_DEDUP          } from '../../../modules/nf-core/sentieon/dedup/main'
-include { SENTIEON_BQSR           } from '../../../modules/local/sentieon/bqsr'
 include { SENTIEON_READWRITER     } from '../../../modules/nf-core/sentieon/readwriter/main'
 workflow ALIGN_SENTIEON {
     take:
         ch_reads_input     // channel: [mandatory] [ val(meta), path(reads_input) ]
         ch_genome_fasta    // channel: [mandatory] [ val(meta), path(fasta) ]
         ch_genome_fai      // channel: [mandatory] [ val(meta), path(fai) ]
         ch_bwa_index       // channel: [mandatory] [ val(meta), path(bwa_index) ]
-        ch_known_dbsnp     // channel: [optional] [ path(known_dbsnp) ]
-        ch_known_dbsnp_tbi // channel: [optional] [ path(known_dbsnp_tbi) ]
         val_platform       // string:  [mandatory] default: illumina
 
     main:
         ch_versions = Channel.empty()
-        ch_bqsr_bam = Channel.empty()
-        ch_bqsr_bai = Channel.empty()
-        ch_bqsr_csv = Channel.empty()
 
         SENTIEON_BWAMEM ( ch_reads_input, ch_bwa_index, ch_genome_fasta.map{ meta, fasta -> fasta }, ch_genome_fai.map{ meta, fai -> fai })
 
@@ -46,27 +40,13 @@ workflow ALIGN_SENTIEON {
 
         SENTIEON_DEDUP ( ch_bam_bai, ch_genome_fasta, ch_genome_fai )
 
-        if (params.variant_caller == "sentieon") {
-            SENTIEON_DEDUP.out.bam
-                .join(SENTIEON_DEDUP.out.bai, failOnMismatch:true, failOnDuplicate:true)
-                .set { ch_dedup_bam_bai }
-            SENTIEON_BQSR ( ch_dedup_bam_bai, ch_genome_fasta, ch_genome_fai, ch_known_dbsnp, ch_known_dbsnp_tbi )
-            ch_bqsr_bam = SENTIEON_BQSR.out.bam
-            ch_bqsr_bai = SENTIEON_BQSR.out.bai
-            ch_bqsr_csv = SENTIEON_BQSR.out.recal_csv
-            ch_versions = ch_versions.mix(SENTIEON_BQSR.out.versions.first())
-        }
-
         ch_versions = ch_versions.mix(SENTIEON_BWAMEM.out.versions.first())
         ch_versions = ch_versions.mix(SENTIEON_DATAMETRICS.out.versions.first())
         ch_versions = ch_versions.mix(SENTIEON_DEDUP.out.versions.first())
 
     emit:
         marked_bam  = SENTIEON_DEDUP.out.bam                             // channel: [ val(meta), path(bam) ]
         marked_bai  = SENTIEON_DEDUP.out.bai                             // channel: [ val(meta), path(bai) ]
-        recal_bam   = ch_bqsr_bam.ifEmpty(null)                          // channel: [ val(meta), path(bam) ]
-        recal_bai   = ch_bqsr_bai.ifEmpty(null)                          // channel: [ val(meta), path(bai) ]
-        recal_csv   = ch_bqsr_csv.ifEmpty(null)                          // channel: [ val(meta), path(csv) ]
         mq_metrics  = SENTIEON_DATAMETRICS.out.mq_metrics.ifEmpty(null)  // channel: [ val(meta), path(mq_metrics) ]
         qd_metrics  = SENTIEON_DATAMETRICS.out.qd_metrics.ifEmpty(null)  // channel: [ val(meta), path(qd_metrics) ]
         gc_metrics  = SENTIEON_DATAMETRICS.out.gc_metrics.ifEmpty(null)  // channel: [ val(meta), path(gc_metrics) ]

diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf
@@ -300,8 +300,6 @@ workflow RAREDISEASE {
         ch_genome_fai,
         ch_genome_bwaindex,
         ch_genome_bwamem2index,
-        ch_dbsnp,
-        ch_dbsnp_tbi,
         params.platform
     )
     .set { ch_mapped }
-Original file line number
+Diff line change
@@ Expand Up / @@ -45,7 +45,4 @@ process { @@
             ]
         }
-        withName: '.*ALIGN:ALIGN_SENTIEON:SENTIEON_BQSR' {
-            ext.prefix = { "${meta.id}_bqsr" }
-        }
     }