nf-core · ramprasadn · Jan 29, 2025 · Jan 29, 2025 · Jan 29, 2025 · Jan 29, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
+- Only Structural variants that PASS the filter will be reported and annotated [#673](https://github.com/nf-core/raredisease/pull/673)
 - Update haplogrep to v3.2.2 [#672](https://github.com/nf-core/raredisease/pull/672)
 - d4 files are not generated by default anymore [#648](https://github.com/nf-core/raredisease/pull/648)
 - Suffix used to identify unique fastq pairs from "\_T" to "\_LNUMBER" [#638](https://github.com/nf-core/raredisease/pull/638)

diff --git a/conf/modules/call_sv_cnvnator.config b/conf/modules/call_sv_cnvnator.config
@@ -37,6 +37,16 @@ process {
         ext.args = { "-call ${params.cnvnator_binsize}" }
     }
 
+    withName: ".*CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:CNVNATOR_CONVERT2VCF" {
+        ext.prefix = { "${meta.id}_cnvnator" }
+        ext.args = { "-call ${params.cnvnator_binsize}" }
+    }
+
+    withName: ".*CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:BCFTOOLS_VIEW_CNVNATOR" {
+        ext.prefix = { "${meta.id}_cnvnator_filter" }
+        ext.args = { '--apply-filters .,PASS --output-type z' }
+    }
+
     withName: '.*CALL_STRUCTURAL_VARIANTS:CALL_SV_CNVNATOR:SVDB_MERGE_CNVNATOR' {
         ext.args   = '--notag --pass_only'
         ext.prefix = { "${meta.id}_cnvnator" }

diff --git a/conf/modules/call_sv_germlinecnvcaller.config b/conf/modules/call_sv_germlinecnvcaller.config
@@ -32,7 +32,7 @@ process {
 
     withName: '.*CALL_STRUCTURAL_VARIANTS:CALL_SV_GERMLINECNVCALLER:BCFTOOLS_VIEW' {
         ext.prefix = { "${meta.id}_gatkcnv_segments_refiltered" }
-        ext.args = { '--output-type z --exclude "N_ALT = 0" ' }
+        ext.args = { '--output-type z --exclude "N_ALT = 0" --apply-filters .,PASS --output-type z' }
     }
 
     withName: '.*CALL_STRUCTURAL_VARIANTS:CALL_SV_GERMLINECNVCALLER:SVDB_MERGE_GCNVCALLER' {

diff --git a/conf/modules/call_sv_manta.config b/conf/modules/call_sv_manta.config
@@ -18,6 +18,9 @@
 process {
     withName: '.*CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:MANTA' {
         ext.args = { (params.analysis_type == "wes") ? '--exome' : '' }
+    }
+    withName: ".*CALL_STRUCTURAL_VARIANTS:CALL_SV_MANTA:BCFTOOLS_VIEW_MANTA" {
         ext.prefix = { "${meta.id}_manta" }
+        ext.args = { '--apply-filters .,PASS --output-type z' }
     }
 }
diff --git a/conf/modules/call_sv_tiddit.config b/conf/modules/call_sv_tiddit.config
@@ -20,6 +20,11 @@ process {
         ext.args   = '-p 6'
     }
 
+    withName: ".*CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:BCFTOOLS_VIEW_TIDDIT" {
+        ext.prefix = { "${meta.id}_tiddit" }
+        ext.args = { '--apply-filters .,PASS --output-type z' }
+    }
+
     withName: '.*CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT' {
         ext.args   = '--notag --pass_only'
         ext.prefix = { "${meta.id}_tiddit" }

diff --git a/subworkflows/local/call_snv.nf b/subworkflows/local/call_snv.nf
@@ -45,6 +45,7 @@ workflow CALL_SNV {
         ch_deepvar_gtbi  = Channel.empty()
         ch_mt_vcf        = Channel.empty()
         ch_mt_tabix      = Channel.empty()
+        ch_mt_txt        = Channel.empty()
         ch_sentieon_vcf  = Channel.empty()
         ch_sentieon_tbi  = Channel.empty()
         ch_sentieon_gvcf = Channel.empty()
@@ -132,7 +133,7 @@ workflow CALL_SNV {
             )
             ch_mt_vcf   = POSTPROCESS_MT_CALLS.out.vcf
             ch_mt_tabix = POSTPROCESS_MT_CALLS.out.tbi
-            ch_mt_txt = CALL_SNV_MT.out.txt
+            ch_mt_txt   = CALL_SNV_MT.out.txt
             ch_versions = ch_versions.mix(CALL_SNV_MT.out.versions)
             ch_versions = ch_versions.mix(CALL_SNV_MT_SHIFT.out.versions)
             ch_versions = ch_versions.mix(POSTPROCESS_MT_CALLS.out.versions)

diff --git a/subworkflows/local/call_structural_variants.nf b/subworkflows/local/call_structural_variants.nf
@@ -37,7 +37,7 @@ workflow CALL_STRUCTURAL_VARIANTS {
 
         if (!params.analysis_type.equals("mito")) {
             CALL_SV_MANTA (ch_genome_bam, ch_genome_bai, ch_genome_fasta, ch_genome_fai, ch_case_info, ch_target_bed)
-                .diploid_sv_vcf
+                .filtered_diploid_sv_vcf_tbi
                 .collect{it[1]}
                 .set{ manta_vcf }
             ch_versions = ch_versions.mix(CALL_SV_MANTA.out.versions)

diff --git a/subworkflows/local/call_sv_cnvnator/main.nf b/subworkflows/local/call_sv_cnvnator/main.nf
@@ -2,14 +2,14 @@
 // A subworkflow to call CNVs using cnvnator
 //
 
-nextflow.enable.dsl = 2
-
 include { CNVNATOR_CNVNATOR as CNVNATOR_RD        } from '../../../modules/nf-core/cnvnator/cnvnator/main.nf'
 include { CNVNATOR_CNVNATOR as CNVNATOR_HIST      } from '../../../modules/nf-core/cnvnator/cnvnator/main.nf'
 include { CNVNATOR_CNVNATOR as CNVNATOR_STAT      } from '../../../modules/nf-core/cnvnator/cnvnator/main.nf'
 include { CNVNATOR_CNVNATOR as CNVNATOR_PARTITION } from '../../../modules/nf-core/cnvnator/cnvnator/main.nf'
 include { CNVNATOR_CNVNATOR as CNVNATOR_CALL      } from '../../../modules/nf-core/cnvnator/cnvnator/main.nf'
 include { CNVNATOR_CONVERT2VCF                    } from '../../../modules/nf-core/cnvnator/convert2vcf/main.nf'
+include { TABIX_BGZIPTABIX as INDEX_CNVNATOR      } from '../../../modules/nf-core/tabix/bgziptabix/main'
+include { BCFTOOLS_VIEW as BCFTOOLS_VIEW_CNVNATOR } from '../../../modules/nf-core/bcftools/view/main.nf'
 include { SVDB_MERGE as SVDB_MERGE_CNVNATOR       } from '../../../modules/nf-core/svdb/merge/main'
 
 workflow CALL_SV_CNVNATOR {
@@ -27,7 +27,9 @@ workflow CALL_SV_CNVNATOR {
         CNVNATOR_STAT ( [[:],[],[]], CNVNATOR_HIST.out.root, [[:],[]], [[:],[]], "stat" )
         CNVNATOR_PARTITION ( [[:],[],[]], CNVNATOR_STAT.out.root, [[:],[]], [[:],[]], "partition" )
         CNVNATOR_CALL ( [[:],[],[]], CNVNATOR_PARTITION.out.root, [[:],[]], [[:],[]], "call" )
-        CNVNATOR_CONVERT2VCF (CNVNATOR_CALL.out.tab).vcf
+        CNVNATOR_CONVERT2VCF (CNVNATOR_CALL.out.tab)
+        INDEX_CNVNATOR (CNVNATOR_CONVERT2VCF.out.vcf)
+        BCFTOOLS_VIEW_CNVNATOR (INDEX_CNVNATOR.out.gz_tbi, [], [], []).vcf
             .collect{it[1]}
             .toList()
             .set { vcf_file_list }
@@ -45,6 +47,8 @@ workflow CALL_SV_CNVNATOR {
         ch_versions = ch_versions.mix(CNVNATOR_CALL.out.versions)
         ch_versions = ch_versions.mix(CNVNATOR_CONVERT2VCF.out.versions)
         ch_versions = ch_versions.mix(SVDB_MERGE_CNVNATOR.out.versions)
+        ch_versions = ch_versions.mix(INDEX_CNVNATOR.out.versions)
+        ch_versions = ch_versions.mix(BCFTOOLS_VIEW_CNVNATOR.out.versions)
 
     emit:
         vcf        = SVDB_MERGE_CNVNATOR.out.vcf  // channel: [ val(meta), path(*.tar.gz) ]

diff --git a/subworkflows/local/call_sv_manta/main.nf b/subworkflows/local/call_sv_manta/main.nf
@@ -2,7 +2,8 @@
 // A structural variant caller workflow for manta
 //
 
-include { MANTA_GERMLINE as MANTA } from '../../../modules/nf-core/manta/germline/main'
+include { MANTA_GERMLINE as MANTA              } from '../../../modules/nf-core/manta/germline/main'
+include { BCFTOOLS_VIEW as BCFTOOLS_VIEW_MANTA } from '../../../modules/nf-core/bcftools/view/main.nf'
 
 workflow CALL_SV_MANTA {
     take:
@@ -41,7 +42,13 @@ workflow CALL_SV_MANTA {
             MANTA ( manta_input, ch_genome_fasta, ch_genome_fai, [] )
         }
 
+        MANTA.out.diploid_sv_vcf
+            .join(MANTA.out.diploid_sv_vcf_tbi)
+            .set {ch_filter_in}
+        BCFTOOLS_VIEW_MANTA (ch_filter_in, [], [], [])
+
         ch_versions = MANTA.out.versions
+        ch_versions = ch_versions.mix(BCFTOOLS_VIEW_MANTA.out.versions)
 
     emit:
         candidate_small_indels_vcf     = MANTA.out.candidate_small_indels_vcf     // channel: [ val(meta), path(vcf) ]
@@ -50,5 +57,6 @@ workflow CALL_SV_MANTA {
         candidate_sv_vcf_tbi           = MANTA.out.candidate_sv_vcf_tbi           // channel: [ val(meta), path(tbi) ]
         diploid_sv_vcf                 = MANTA.out.diploid_sv_vcf                 // channel: [ val(meta), path(vcf) ]
         diploid_sv_vcf_tbi             = MANTA.out.diploid_sv_vcf_tbi             // channel: [ val(meta), path(tbi) ]
+        filtered_diploid_sv_vcf_tbi    = BCFTOOLS_VIEW_MANTA.out.vcf              // channel: [ val(meta), path(vcf), path(tbi) ]
         versions                       = ch_versions
 }
diff --git a/subworkflows/local/call_sv_tiddit/main.nf b/subworkflows/local/call_sv_tiddit/main.nf
@@ -2,8 +2,10 @@
 // A structural variant caller workflow for tiddit
 //
 
-include { TIDDIT_SV                       } from '../../../modules/nf-core/tiddit/sv/main'
-include { SVDB_MERGE as SVDB_MERGE_TIDDIT } from '../../../modules/nf-core/svdb/merge/main'
+include { TIDDIT_SV                             } from '../../../modules/nf-core/tiddit/sv/main'
+include { SVDB_MERGE as SVDB_MERGE_TIDDIT       } from '../../../modules/nf-core/svdb/merge/main'
+include { TABIX_BGZIPTABIX as INDEX_TIDDIT      } from '../../../modules/nf-core/tabix/bgziptabix/main'
+include { BCFTOOLS_VIEW as BCFTOOLS_VIEW_TIDDIT } from '../../../modules/nf-core/bcftools/view/main.nf'
 
 workflow CALL_SV_TIDDIT {
     take:
@@ -15,8 +17,8 @@ workflow CALL_SV_TIDDIT {
     main:
         TIDDIT_SV ( ch_bam_bai, ch_genome_fasta, ch_bwa_index )
 
-        TIDDIT_SV.out
-            .vcf
+        INDEX_TIDDIT (TIDDIT_SV.out.vcf)
+        BCFTOOLS_VIEW_TIDDIT (INDEX_TIDDIT.out.gz_tbi, [], [], []).vcf
             .collect{it[1]}
             .toList()
             .set { vcf_file_list }
@@ -29,6 +31,8 @@ workflow CALL_SV_TIDDIT {
 
         ch_versions = TIDDIT_SV.out.versions.first()
         ch_versions = ch_versions.mix(SVDB_MERGE_TIDDIT.out.versions)
+        ch_versions = ch_versions.mix(INDEX_TIDDIT.out.versions)
+        ch_versions = ch_versions.mix(BCFTOOLS_VIEW_TIDDIT.out.versions)
 
     emit:
         vcf      = SVDB_MERGE_TIDDIT.out.vcf // channel: [ val(meta), path(vcf) ]