sort annotsv VCFs

CHANGELOG.md

@@ -28,6 +28,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 1. Fail the pipeline when the sex determination failed. This will now prompt the user to add the sex to the samplesheet so the pipeline doesn't do any wrong assumptions
 2. Fixed the Jasmine module output VCFs being empty when no variants have been merged. This file now contains the header of one of the input VCFs
+3. AnnotSV VCF files are now sorted before trying to combine it with the VEP output.
 
 ## v0.2.0 - [19 July 2024] - Mighty Manneken Pis
 

conf/modules.config

@@ -221,10 +221,15 @@ process {
     }
 
     withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV:BCFTOOLS_CONCAT\$" {
-        ext.prefix = "annotsv_annotated"
+        ext.prefix = "annotsv_annotated_unsorted"
         ext.args = "--output-type z --naive-force"
     }
 
+    withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV:BCFTOOLS_SORT\$" {
+        ext.prefix = "annotsv_annotated"
+        ext.args = "--output-type z --write-index=tbi"
+    }
+
     withName: "^.*VCF_ANNOTATE_VEP_ANNOTSV:ENSEMBLVEP_VEP\$" {
         ext.prefix = {"${meta.id}.vep"}
         ext.args = {[

subworkflows/local/vcf_annotate_vep_annotsv/main.nf

@@ -11,6 +11,7 @@ include { TABIX_TABIX as TABIX_ANNOTSV              } from '../../../modules/nf-
 include { TABIX_TABIX as TABIX_VEP                  } from '../../../modules/nf-core/tabix/tabix/main'
 include { BCFTOOLS_FILTER                           } from '../../../modules/nf-core/bcftools/filter/main'
 include { BCFTOOLS_CONCAT                           } from '../../../modules/nf-core/bcftools/concat/main'
+include { BCFTOOLS_SORT                             } from '../../../modules/nf-core/bcftools/sort/main'
 
 workflow VCF_ANNOTATE_VEP_ANNOTSV {
     take:
@@ -104,13 +105,13 @@ workflow VCF_ANNOTATE_VEP_ANNOTSV {
     )
     ch_versions = ch_versions.mix(BCFTOOLS_CONCAT.out.versions.first())
 
-    TABIX_ANNOTSV(
+    BCFTOOLS_SORT(
         BCFTOOLS_CONCAT.out.vcf
     )
-    ch_versions = ch_versions.mix(TABIX_ANNOTSV.out.versions.first())
+    ch_versions = ch_versions.mix(BCFTOOLS_SORT.out.versions.first())
 
-    def ch_annotsv_output = BCFTOOLS_CONCAT.out.vcf
-        .join(TABIX_ANNOTSV.out.tbi, failOnDuplicate:true, failOnMismatch:true)
+    def ch_annotsv_output = BCFTOOLS_SORT.out.vcf
+        .join(BCFTOOLS_SORT.out.tbi, failOnDuplicate:true, failOnMismatch:true)
 
     ENSEMBLVEP_VEP(
         ch_vcfs,