2.3.0 - Getafix

What's Changed

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

New Contributors

• @fevac made their first contribution in #662

Full Changelog: 2.2.0...2.3.0