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update CHANGELOG
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maxulysse committed Jun 21, 2022
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Expand Up @@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#557](https://github.com/nf-core/sarek/pull/557) - Add `Haplotypecaller` single sample mode together with `CNNScoreVariants` and `FilterVariantTranches`
- [#576](https://github.com/nf-core/sarek/pull/576) - Add modules and subworkflows for `cnvkit` germline mode
- [#582](https://github.com/nf-core/sarek/pull/582) - Added option `--vep_out_format` for setting the format of the output-file from VEP to `json`, `tab` or `vcf` (default)
- [#600](https://github.com/nf-core/sarek/pull/600) - Added description for UMI related params in schema

### Changed

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- [#585](https://github.com/nf-core/sarek/pull/585) - Remove explicit BAM to CRAM conversion after MarkduplicatesSpark; tool does it internally
- [#581](https://github.com/nf-core/sarek/pull/581) - `TIDDIT` is updated to `3.1.0`
- [#593](https://github.com/nf-core/sarek/pull/593) - update `ensembl-vep` cache version and module
- [#600](https://github.com/nf-core/sarek/pull/600) - Remove `TODO` in awsfulltest

### Fixed

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- [#590](https://github.com/nf-core/sarek/pull/590) - Fix empty folders during scatter/gather
- [#592](https://github.com/nf-core/sarek/pull/592) - Fix optional resources for Mutect2, GetPileupSummaries, and HaplotypeCaller: issue [#299](https://github.com/nf-core/sarek/issues/299), [#359](https://github.com/nf-core/sarek/issues/359), [#367](https://github.com/nf-core/sarek/issues/367)
- [#598](https://github.com/nf-core/sarek/pull/598) - Remove WARNING message for config selector not matching
- [#600](https://github.com/nf-core/sarek/pull/600) - Remove `nf-core lint` warnings

### Deprecated

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