Merge branch 'dev' into sarek_bcftools_norm

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "nextflow.formatting.harshilAlignment": true
+}

CHANGELOG.md

@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [1664](https://github.com/nf-core/sarek/pull/1664) - Check if flowcell ID matches for read pair
 - [1663](https://github.com/nf-core/sarek/pull/1663) - Massive conda modules update
 - [1680](https://github.com/nf-core/sarek/pull/1682) - Add `bcftools_norm` in `POST_VARIANTCALLING` for normalization of all vcf files or for concatenated germline vcfs
+- [1730](https://github.com/nf-core/sarek/pull/1730) - Enable Harshil Alignment™️ in VS Code workspace settings
 
 ### Changed
 
@@ -29,9 +30,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [1695](https://github.com/nf-core/sarek/pull/1695) - Update all modules
 - [1707](https://github.com/nf-core/sarek/pull/1707) - Un-hide parameters and clean up Json schema
 - [1708](https://github.com/nf-core/sarek/pull/1708) - Migrate pipeline pytest alignment and annotation tests to nf-test
+- [1711](https://github.com/nf-core/sarek/pull/1711) - Migrate pipeline pytest strelka tests to nf-test
 
 ### Fixed
 
+- [1624](https://github.com/nf-core/sarek/pull/1624) - Fix channel stalling for bcftools index
 - [1657](https://github.com/nf-core/sarek/pull/1657) - Update all actions used in the GHA CI
 - [1661](https://github.com/nf-core/sarek/pull/1661) - nf-test pipeline level tests
 - [1673](https://github.com/nf-core/sarek/pull/1673) - Print warning message instead of silent error with Nextflow versions prior to 24.08.0edge
@@ -45,6 +48,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [1656](https://github.com/nf-core/sarek/pull/1656) - Retiring parameter `snpeff_genome`
 - [1709](https://github.com/nf-core/sarek/pull/1709) - Remove `Strelka` tumor-only somatic variant calling
+- [1728](https://github.com/nf-core/sarek/pull/1728) - Remove BAM to CRAM conversion of input files for post-alignment entry points
 
 ### Dependencies
 
@@ -108,7 +112,7 @@ Loametjåhkkå is another one of the main peaks of the Pårte massif.
 ### Added
 
 - [#1502](https://github.com/nf-core/sarek/pull/1502) - export CNVs into VCF format in `bam_variant_calling_cnvkit`
-- [#1534](https://github.com/nf-core/sarek/pull/1534), [#1573](https://github.com/nf-core/sarek/pull/1573) - Handling `.fastq.gz.spring` files as input
+- [#1534](https://github.com/nf-core/sarek/pull/1534), [#1573](https://github.com/nf-core/sarek/pull/1573), [#1734](https://github.com/nf-core/sarek/pull/1534) - Handling `.fastq.gz.spring` files as input
 - [#1593](https://github.com/nf-core/sarek/pull/1593) - Prepare release `3.4.2`
 
 ### Changed