fix(postprocess_mt_calls): split multiallelics after bcftools merge

CHANGELOG.md

@@ -3,6 +3,41 @@
 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).
 
+## 3.0.1 - Mario-patch [2026-05-25]
+
+### `Added`
+
+- Parameter `cadd_prescored` to pass a directory of pre-scored CADD indel annotations to the CADD process in genome and mitochondrial SNV annotation subworkflows [#866](https://github.com/nf-core/raredisease/pull/866)
+- Parameter `manta_call_regions` to restrict Manta SV calling to specified regions (e.g. primary chromosomes) via a bgzipped, tabix-indexed BED file, reducing runtime without affecting other callers [#867](https://github.com/nf-core/raredisease/pull/867)
+- Local `FILTERVEP` module using a Python reimplementation of Ensembl's `filter_vep`, replacing the `ENSEMBLVEP_FILTERVEP` module with a lighter cyvcf2-based alternative [#870](https://github.com/nf-core/raredisease/pull/870)
+- `bwafastalign/index` nf-core module and `bwafastalign` parameter to support index preparation for the bwa-fastalign genome aligner [#877](https://github.com/nf-core/raredisease/pull/877)
+- `bwafastalign/mem` nf-core module to support genome alignment with bwa-fastalign when `--aligner bwafastalign` is set [#880](https://github.com/nf-core/raredisease/pull/880)
+
+### `Changed`
+
+- Replace `ENSEMBLVEP_FILTERVEP` with local `FILTERVEP` in the clinical set subworkflow, renamed from `VCF_FILTER_BCFTOOLS_ENSEMBLVEP` to `VCF_FILTER_BCFTOOLS_FILTERVEP` [#870](https://github.com/nf-core/raredisease/pull/870)
+- Increase default mbuffer memory value from 3GB to 8GB [#880](https://github.com/nf-core/raredisease/pull/880)
+- Update `bwameme/mem` to new nf-core module signature: `val mbuffer` and `val samtools_threads` replaced by `ext.args2` and `ext.args3` [#881](https://github.com/nf-core/raredisease/pull/881)
+
+### `Fixed`
+
+- Add a bcftools norm split-multiallelics step after merging standard and shifted MT calls to handle new multiallelic sites introduced by bcftools merge [#855](https://github.com/nf-core/raredisease/pull/855)
+
+### Parameters
+
+| Old parameter | New parameter          |
+| ------------- | ---------------------- |
+|               | bwafastalign           |
+|               | cadd_prescored         |
+|               | manta_call_regions     |
+|               | manta_call_regions_tbi |
+
+### Tool updates
+
+| Tool          | Old version | New version |
+| ------------- | ----------- | ----------- |
+| bwa-fastalign |             | 1.0.0       |
+
 ## 3.0.0 - Mario [2026-05-12]
 
 ### `Added`
@@ -121,6 +156,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | picard                | 3.3.0       | 3.4.0       |
 | pigz                  | 2.3.4       | 2.8         |
 | qualimap              | 2.3         |             |
+| saltshaker            | 1.0.0       | 1.1.1       |
 | sambamba              |             | 1.0.1       |
 | samtools              | 1.21        | 1.22.1      |
 | sentieon              | 202503      | 202503.02   |