What's Changed

* Annotate small indels with CADD scores by @ramprasadn in https://github.com/nf-core/raredisease/pull/325

* convert bam to cram by @ramprasadn in https://github.com/nf-core/raredisease/pull/340

* Add shiftfasta by @ramprasadn in https://github.com/nf-core/raredisease/pull/354

* feat added MT deletion script by @Lucpen in https://github.com/nf-core/raredisease/pull/349

* Adding upd by @hrydbeck in https://github.com/nf-core/raredisease/pull/364

* Add ek by @Lucpen in https://github.com/nf-core/raredisease/pull/365

* add chromograph by @ramprasadn in https://github.com/nf-core/raredisease/pull/366

* Update to template 2.9 by @ramprasadn in https://github.com/nf-core/raredisease/pull/372

* Avoid publishing uncompressed VCF-file from HMTNOTE_ANNOTATE by @asp8200 in https://github.com/nf-core/raredisease/pull/368

* added check for case id by @EmmaCAndersson in https://github.com/nf-core/raredisease/pull/357

* Gatkcnvcaller by @ramprasadn in https://github.com/nf-core/raredisease/pull/362

* Update schema, output.md, and remove unused parameters by @ramprasadn in https://github.com/nf-core/raredisease/pull/373

* update eklipse by @ramprasadn in https://github.com/nf-core/raredisease/pull/374

New Contributors

* @adamrtalbot made their first contribution in https://github.com/nf-core/raredisease/pull/360

* @hrydbeck made their first contribution in https://github.com/nf-core/raredisease/pull/364

* @asp8200 made their first contribution in https://github.com/nf-core/raredisease/pull/368

* @EmmaCAndersson made their first contribution in https://github.com/nf-core/raredisease/pull/357

*Full Changelog*: https://github.com/nf-core/raredisease/compare/1.0.0...1.1.0