Merge pull request #2137 from nf-core/dev

Author: FriederikeHanssen

.nf-core.yml

@@ -23,4 +23,4 @@ template:
   name: sarek
   org: nf-core
   outdir: .
-  version: 3.8.0
+  version: 3.8.1

CHANGELOG.md

@@ -5,6 +5,40 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [3.8.1](https://github.com/nf-core/sarek/releases/tag/3.8.1) - Laitaure
+
+### Added
+
+### Changed
+
+### Fixed
+
+- [#2128](https://github.com/nf-core/sarek/pull/2128) - Fix `bcftools concat` failing on Strelka somatic VCFs with non-contiguous chromosome blocks by adding `--allow-overlaps`
+
+### Removed
+
+### Dependencies
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+
+### Parameters
+
+| Params | status |
+| ------ | ------ |
+
+### Developer section
+
+#### Added
+
+#### Changed
+
+- [#2134](https://github.com/nf-core/sarek/pull/2134) - Back to dev (3.9.0dev)
+
+#### Fixed
+
+#### Removed
+
 ## [3.8.0](https://github.com/nf-core/sarek/releases/tag/3.8.0) - Sitojaure
 
 A mountain cabin near the Sami settlement between Saltoluokta and Kvikkjokk.
@@ -30,6 +64,7 @@ A mountain cabin near the Sami settlement between Saltoluokta and Kvikkjokk.
 - [#2099](https://github.com/nf-core/sarek/pull/2099) - Remove deprecated `msisensor2_scan` parameter from schema and igenomes config to fix `nf-core pipelines schema build` validation error
 - [#2100](https://github.com/nf-core/sarek/pull/2100) - Add missing citations for Condel, Mastermind, goleft indexcov, NGSCheckMate, SPRING, and vcflib to CITATIONS.md
 - [#2109](https://github.com/nf-core/sarek/pull/2109) - Fix consensus calling to capture all variants from all callers by using `sites.txt` output; adds `CALLERS` and `NCALLERS` INFO fields to consensus VCF
+- [#2113](https://github.com/nf-core/sarek/pull/2113) - Fix regex patterns for `dbnsfp_tbi`, `spliceai_snv`, and `spliceai_snv_tbi` parameter validation
 
 ### Removed
 
@@ -193,7 +228,6 @@ This patch release includes a bump to Nextflow 25.04.8.
 
 ### Fixed
 
-- [#2050](https://github.com/nf-core/sarek/issues/2050) - Fix regex patterns for `dbnsfp_tbi`, `spliceai_snv`, and `spliceai_snv_tbi` parameter validation
 - [2029](https://github.com/nf-core/sarek/pull/2029) - Correct intervals channel for parabricks
 
 ### Removed

assets/multiqc_config.yml

@@ -3,7 +3,7 @@ custom_logo_url: https://github.com/nf-core/sarek/
 custom_logo_title: "nf-core/sarek"
 
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/sarek/releases/tag/3.8.0" target="_blank">nf-core/sarek</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/sarek/3.8.0/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/sarek/releases/tag/3.8.1" target="_blank">nf-core/sarek</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/sarek/3.8.1/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-sarek-methods-description":
     order: -1000

conf/modules/post_variant_calling.config

@@ -59,7 +59,7 @@ process {
     }
 
     withName: 'NFCORE_SAREK:SAREK:POST_VARIANTCALLING:CONSENSUS:BCFTOOLS_CONCAT' {
-        ext.args   = { "--output-type z --write-index=tbi" }
+        ext.args   = { "--output-type z --write-index=tbi --allow-overlaps" }
         ext.prefix = { "${meta.id}.strelka" }
         publishDir = [ enabled: false ]
     }

nextflow.config

@@ -723,7 +723,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
     nextflowVersion = '!>=25.10.2'
-    version         = '3.8.0'
+    version         = '3.8.1'
     doi             = '10.12688/f1000research.16665.2, 10.1093/nargab/lqae031, 10.5281/zenodo.3476425'
 }