What's Changed Bumpversion 2.2.0->2.3.0dev by @ramprasadn in https://github.com/nf-core/raredisease/pull/610 Add option to analyse only mitochondria by @ramprasadn in https://github.com/nf-core/raredisease/pull/608 5% frequency threshold for mitochondrial clinical vcfs by @ramprasadn in https://github.com/nf-core/raredisease/pull/616 allow vep 112 by @jemten in https://github.com/nf-core/raredisease/pull/617 Minor fixes by @ramprasadn in https://github.com/nf-core/raredisease/pull/618 update modules by @ramprasadn in https://github.com/nf-core/raredisease/pull/619 Change output file prefix for upd and chromograph by @ramprasadn in https://github.com/nf-core/raredisease/pull/620 Invoke rhocallviz subworkflow only once per sample. by @ramprasadn in https://github.com/nf-core/raredisease/pull/621 Update modules by @ramprasadn in https://github.com/nf-core/raredisease/pull/623 Fix channel declaration error in the cadd subworkflow by @ramprasadn in https://github.com/nf-core/raredisease/pull/624 Update genmod and multiqc by @ramprasadn in https://github.com/nf-core/raredisease/pull/625 template update 3.0.1 by @ramprasadn in https://github.com/nf-core/raredisease/pull/629 Important! Template update for nf-core/tools v3.0.1 by @nf-core-bot in https://github.com/nf-core/raredisease/pull/628 Important! Template update for nf-core/tools v3.0.2 by @nf-core-bot in https://github.com/nf-core/raredisease/pull/630 ensure string comparison by @jemten in https://github.com/nf-core/raredisease/pull/632 add bait regions to deepvariant for WES by @ramprasadn in https://github.com/nf-core/raredisease/pull/633 Merge germlinecnvcaller output by @ramprasadn in https://github.com/nf-core/raredisease/pull/635 Raredisease: Add fastp output to multiqc by @peterpru in https://github.com/nf-core/raredisease/pull/637 Fix fastqc samplenames in multiqc report by @ramprasadn in https://github.com/nf-core/raredisease/pull/638 Vep update to 113 by @ramprasadn in https://github.com/nf-core/raredisease/pull/639 Use target bed files as regions instead of bait intervals for SNV calling in WES samples by @ramprasadn in https://github.com/nf-core/raredisease/pull/636 Upd fix by @jemten in https://github.com/nf-core/raredisease/pull/643 Update modules by @ramprasadn in https://github.com/nf-core/raredisease/pull/646 Add option to restrict analysis to specific contigs by @ramprasadn in https://github.com/nf-core/raredisease/pull/644 add fastp and ngsbits to multiqc input by @peterpru in https://github.com/nf-core/raredisease/pull/647 Fix tests by @ramprasadn in https://github.com/nf-core/raredisease/pull/648 patch vep 110 by @ramprasadn in https://github.com/nf-core/raredisease/pull/649 Sync v3.1.1 of nf-core template by @ramprasadn in https://github.com/nf-core/raredisease/pull/655 Important! Template update for nf-core/tools v3.1.1 by @nf-core-bot in https://github.com/nf-core/raredisease/pull/654 Remove suffixes sample name in repeat call vcfs by @ramprasadn in https://github.com/nf-core/raredisease/pull/657 Update module MultiQC to version 1.26 by @peterpru in https://github.com/nf-core/raredisease/pull/660 padding bed file by @jemten in https://github.com/nf-core/raredisease/pull/658 Fix sex by @jemten in https://github.com/nf-core/raredisease/pull/659 Pre release PR1 by @ramprasadn in https://github.com/nf-core/raredisease/pull/664 set meta.id for some input files by @jemten in https://github.com/nf-core/raredisease/pull/661 Add haplocheck to multiqc by @fevac in https://github.com/nf-core/raredisease/pull/662 Pre release PR2 by @ramprasadn in https://github.com/nf-core/raredisease/pull/665 Fix download tests by @ramprasadn in https://github.com/nf-core/raredisease/pull/667 Important! Template update for nf-core/tools v3.1.2 by @nf-core-bot in https://github.com/nf-core/raredisease/pull/668 Review suggestions on v2.3.0 by @ramprasadn in https://github.com/nf-core/raredisease/pull/669 Template update v320 by @ramprasadn in https://github.com/nf-core/raredisease/pull/671 Important! Template update for nf-core/tools v3.2.0 by @nf-core-bot in https://github.com/nf-core/raredisease/pull/670 update haplogrep3 by @ramprasadn in https://github.com/nf-core/raredisease/pull/672 Keep only SVs that PASS the filter by @ramprasadn in https://github.com/nf-core/raredisease/pull/673 Update versions by @ramprasadn in https://github.com/nf-core/raredisease/pull/674 Add option to skip haplogrep3 by @ramprasadn in https://github.com/nf-core/raredisease/pull/675 Release v2.3.0 by @ramprasadn in https://github.com/nf-core/raredisease/pull/666 New Contributors @fevac made their first contribution in https://github.com/nf-core/raredisease/pull/662 Full Changelog: https://github.com/nf-core/raredisease/compare/2.2.0...2.3.0