nf-core · famosab · Feb 12, 2026 · Nov 14, 2025 · Nov 14, 2025 · Nov 14, 2025
@@ -11,14 +11,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
+- [#2055](https://github.com/nf-core/sarek/pull/2055) - Sort final vcf in varlociraptor sbwfs and update varlociraptor
+
 ### Fixed
 
 ### Removed
 
 ### Dependencies
 
-| Dependency | Old version | New version |
-| ---------- | ----------- | ----------- |
+| Dependency    | Old version | New version |
+| ------------- | ----------- | ----------- |
+| varlociraptor | 8.7.4       | 8.9.3       |
+| yte           | 1.9.0       | 1.9.4       |
 
 ### Parameters
 
@@ -31,6 +35,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 #### Changed
 
+- [#2055](https://github.com/nf-core/sarek/pull/2055) - Update varlociraptor to use only one input channel, swap to topics
 - [#2139](https://github.com/nf-core/sarek/pull/2139) - Back to dev (3.9.0dev)
 
 #### Fixed
@@ -203,6 +208,7 @@ This release includes a bump to Nextflow 25.10.2.
 
 ### Changed
 
+- [#2045](https://github.com/nf-core/sarek/pull/2045) - Propagate fastp shard naming if exists through BBSplit to ensure unique naming in Markduplicates
 - [#2065](https://github.com/nf-core/sarek/pull/2065) - Bump minimal Nextflow version to 25.10.2
 
 ### Fixed

@@ -22,7 +22,6 @@ process {
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/varlociraptor/${meta.id}/" },
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
@@ -34,7 +33,6 @@ process {
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/varlociraptor/${meta.id}/" },
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
@@ -59,26 +57,34 @@ process {
         ]
     }
 
-    withName: 'SORT_CALLED_CHUNKS' {
+    withName: SORT_CALLED_CHUNKS {
         ext.args   = { '--output-type z --write-index=tbi' }
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/" },
-            saveAs: { params.varlociraptor_chunk_size > 1 ? null : "varlociraptor/${meta.id}/${it}" }
+            saveAs: { file -> params.varlociraptor_chunk_size > 1 ? null : "varlociraptor/${meta.id}/${file}" },
         ]
     }
 
     withName: '.*:VCF_VARLOCIRAPTOR_GERMLINE:SORT_CALLED_CHUNKS' {
-        ext.prefix = { params.varlociraptor_chunk_size > 1 ? "${meta.id}.${meta.variantcaller}.sort.${meta.chunk}" : "${meta.id}.${meta.variantcaller}.germline.varlociraptor"}
+        ext.prefix = { params.varlociraptor_chunk_size > 1 ? "${meta.id}.${meta.variantcaller}.sort.${meta.chunk}" : "${meta.id}.${meta.variantcaller}.germline.varlociraptor" }
     }
 
     withName: '.*:VCF_VARLOCIRAPTOR_TUMOR_ONLY:SORT_CALLED_CHUNKS' {
-        ext.prefix = { params.varlociraptor_chunk_size > 1 ? "${meta.id}.${meta.variantcaller}.sort.${meta.chunk}" : "${meta.id}.${meta.variantcaller}.tumor_only.varlociraptor"}
+        ext.prefix = { params.varlociraptor_chunk_size > 1 ? "${meta.id}.${meta.variantcaller}.sort.${meta.chunk}" : "${meta.id}.${meta.variantcaller}.tumor_only.varlociraptor" }
     }
 
     withName: '.*:VCF_VARLOCIRAPTOR_GERMLINE:CONCAT_CALLED_CHUNKS' {
+        ext.prefix = { "${meta.id}.${meta.variantcaller}.germline.varlociraptor.concat" }
+        ext.args   = { '--allow-overlaps --output-type z' }
+        publishDir = [
+            enabled: false
+        ]
+    }
+
+    withName: '.*:VCF_VARLOCIRAPTOR_GERMLINE:SORT_FINAL_VCF' {
         ext.prefix = { "${meta.id}.${meta.variantcaller}.germline.varlociraptor" }
-        ext.args   = { '--allow-overlaps --output-type z --write-index=tbi' }
+        ext.args   = { '--output-type z --write-index=tbi' }
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/varlociraptor/${meta.id}/" },
@@ -87,8 +93,16 @@ process {
     }
 
     withName: '.*:VCF_VARLOCIRAPTOR_TUMOR_ONLY:CONCAT_CALLED_CHUNKS' {
+        ext.prefix = { "${meta.id}.${meta.variantcaller}.tumor_only.varlociraptor.concat" }
+        ext.args   = { '--allow-overlaps --output-type z' }
+        publishDir = [
+            enabled: false
+        ]
+    }
+
+    withName: '.*:VCF_VARLOCIRAPTOR_TUMOR_ONLY:SORT_FINAL_VCF' {
         ext.prefix = { "${meta.id}.${meta.variantcaller}.tumor_only.varlociraptor" }
-        ext.args   = { '--allow-overlaps --output-type z --write-index=tbi' }
+        ext.args   = { '--output-type z --write-index=tbi' }
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/varlociraptor/${meta.id}/" },
@@ -104,7 +118,6 @@ process {
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/varlociraptor/${meta.id}/" },
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
@@ -126,7 +139,7 @@ process {
 
     withName: '.*:VCF_VARLOCIRAPTOR_SOMATIC:MERGE_GERMLINE_SOMATIC_VCFS' {
         ext.prefix = { "${meta.id}.${meta.variantcaller}.merged" }
-        ext.args   = { '--output-type z' }
+        ext.args   = { '--output-type z --force-samples' }
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/varlociraptor/${meta.id}/" },
@@ -153,7 +166,6 @@ process {
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/varlociraptor/${meta.id}/" },
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
@@ -172,12 +184,20 @@ process {
     }
 
     withName: '.*:VCF_VARLOCIRAPTOR_SOMATIC:SORT_CALLED_CHUNKS' {
-        ext.prefix = { params.varlociraptor_chunk_size > 1 ? "${meta.id}.${meta.variantcaller}.sort.${meta.chunk}" : "${meta.id}.${meta.variantcaller}.somatic.varlociraptor"}
+        ext.prefix = { params.varlociraptor_chunk_size > 1 ? "${meta.id}.${meta.variantcaller}.sort.${meta.chunk}" : "${meta.id}.${meta.variantcaller}.somatic.varlociraptor" }
     }
 
     withName: '.*:VCF_VARLOCIRAPTOR_SOMATIC:CONCAT_CALLED_CHUNKS' {
+        ext.prefix = { "${meta.id}.${meta.variantcaller}.somatic.varlociraptor.concat" }
+        ext.args   = { '--allow-overlaps --output-type z' }
+        publishDir = [
+            enabled: false
+        ]
+    }
+
+    withName: '.*:VCF_VARLOCIRAPTOR_SOMATIC:SORT_FINAL_VCF' {
         ext.prefix = { "${meta.id}.${meta.variantcaller}.somatic.varlociraptor" }
-        ext.args   = { '--allow-overlaps --output-type z --write-index=tbi' }
+        ext.args   = { '--output-type z --write-index=tbi' }
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/varlociraptor/${meta.id}/" },

@@ -413,7 +413,7 @@
                     },
                     "rbt/vcfsplit": {
                         "branch": "master",
-                        "git_sha": "3e5034548e2398b006a9e01fb82673ffa5c83d9f",
+                        "git_sha": "c734c101f0010ec13ed9bbf578477962c32f9cc3",
                         "installed_by": ["modules"]
                     },
                     "samtools/bam2fq": {
@@ -573,17 +573,17 @@
                     },
                     "varlociraptor/callvariants": {
                         "branch": "master",
-                        "git_sha": "36cf856b511b7623a2d90788c9afa2a655fe6d43",
+                        "git_sha": "5ae3c74e09c529c5c768aa89397e490ba4728219",
                         "installed_by": ["modules"]
                     },
                     "varlociraptor/estimatealignmentproperties": {
                         "branch": "master",
-                        "git_sha": "36cf856b511b7623a2d90788c9afa2a655fe6d43",
+                        "git_sha": "5ae3c74e09c529c5c768aa89397e490ba4728219",
                         "installed_by": ["modules"]
                     },
                     "varlociraptor/preprocess": {
                         "branch": "master",
-                        "git_sha": "36cf856b511b7623a2d90788c9afa2a655fe6d43",
+                        "git_sha": "5ae3c74e09c529c5c768aa89397e490ba4728219",
                         "installed_by": ["modules"]
                     },
                     "vcflib/vcffilter": {
@@ -598,7 +598,7 @@
                     },
                     "yte": {
                         "branch": "master",
-                        "git_sha": "b9947fd7a338e1087a5c386ac7192588d3059122",
+                        "git_sha": "c734c101f0010ec13ed9bbf578477962c32f9cc3",
                         "installed_by": ["modules"]
                     }
                 }