Initial release.

What’s Changed

• FEAT: add CNVKIT + base skeleton by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/5
• Update CNVkit/batch by @ramprasadn in https://github.com/nf-core/createpanelrefs/pull/9
• Add germlinecnvcaller by @ramprasadn in https://github.com/nf-core/createpanelrefs/pull/10
• Add optional targets argument to CNVkit by @lescai in https://github.com/nf-core/createpanelrefs/pull/13
• Important! Template update for nf-core/tools v2.11.1 by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/14
• Template updates v2.13 by @ramprasadn in https://github.com/nf-core/createpanelrefs/pull/20
• Important! Template update for nf-core/tools v2.13 by @nf-core-bot in https://github.com/nf-core/createpanelrefs/pull/18
• Template update v2.13.1 by @ramprasadn in https://github.com/nf-core/createpanelrefs/pull/22
• Important! Template update for nf-core/tools v2.13.1 by @nf-core-bot in https://github.com/nf-core/createpanelrefs/pull/21
• update Germlinecnvcaller subworkflow by @ramprasadn in https://github.com/nf-core/createpanelrefs/pull/19
• PON for gens by @ramprasadn in https://github.com/nf-core/createpanelrefs/pull/17
• Adding PON with Mutect2 by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/8
• Refactor + updates to gens and germlinecnvcaller by @ramprasadn in https://github.com/nf-core/createpanelrefs/pull/24
• Important! Template update for nf-core/tools v2.14.0 by @nf-core-bot in https://github.com/nf-core/createpanelrefs/pull/25
• Important! Template update for nf-core/tools v2.14.1 by @nf-core-bot in https://github.com/nf-core/createpanelrefs/pull/26
• updates the default args for gens by @jemten in https://github.com/nf-core/createpanelrefs/pull/28
• update modules by @ramprasadn in https://github.com/nf-core/createpanelrefs/pull/30
• publish gens intervals by default by @jemten in https://github.com/nf-core/createpanelrefs/pull/31
• Important! Template update for nf-core/tools v3.0.2 by @nf-core-bot in https://github.com/nf-core/createpanelrefs/pull/35
• update modules by @ramprasadn in https://github.com/nf-core/createpanelrefs/pull/38
• Use GATK4 to create sequence dictionary instead of Picard by @ramprasadn in https://github.com/nf-core/createpanelrefs/pull/40
• Template update v3.2.0 by @ramprasadn in https://github.com/nf-core/createpanelrefs/pull/45
• cnvkit with cram files by @ramprasadn in https://github.com/nf-core/createpanelrefs/pull/47
• Add automatic shards for nf-test by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/48
• Add tests: CRAM with Mutect2 by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/49
• Important! Template update for nf-core/tools v3.2.1 by @nf-core-bot in https://github.com/nf-core/createpanelrefs/pull/52
• improve some references usage by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/50
• Minor fixes by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/53
• Important! Template update for nf-core/tools v3.3.1 by @nf-core-bot in https://github.com/nf-core/createpanelrefs/pull/54
• prepare RC 1.0.0 by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/55
• fix gcnv interval list by @danielhmendoza01 in https://github.com/nf-core/createpanelrefs/pull/56
• Fix dev according to comments from the release PR by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/57
• Important! Template update for nf-core/tools v3.3.2 by @nf-core-bot in https://github.com/nf-core/createpanelrefs/pull/58
• Address releases comments by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/59
• Important! Template update for nf-core/tools v3.4.1 by @nf-core-bot in https://github.com/nf-core/createpanelrefs/pull/60
• test_full by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/62
• Important! Template update for nf-core/tools v3.5.0dev by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/63
• Important! Template update for nf-core/tools v3.5.1 by @nf-core-bot in https://github.com/nf-core/createpanelrefs/pull/64
• Long-read GENS PON by @fellen31 in https://github.com/nf-core/createpanelrefs/pull/66
• update all modules/subworkflows/plugins by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/69
• Fix conda CI by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/70
• Fix time resource requirement by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/71
• fix time requirement by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/72
• more time for mutect2 by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/73
• Update all modules/subworkflows by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/74
• Important! Template update for nf-core/tools v4.0.1 by @nf-core-bot in https://github.com/nf-core/createpanelrefs/pull/76
• Important! Template update for nf-core/tools v4.0.2 by @nf-core-bot in https://github.com/nf-core/createpanelrefs/pull/77
• add intervals for mutect2 PON by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/78
• Extract alignment indexing into prepare_alignment subworkflow by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/79
• Update all modules and subworkflows by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/80
• Refactor tools handling to use defineToolsList function by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/81
• Fix mutect2_pon_name usage with mutect2 runs by @Copilot in https://github.com/nf-core/createpanelrefs/pull/82
• Refactor tool-specific subworkflows by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/83
• Remove ext.when from germlinecnvcaller_cohort config and handle conditions in subworkflow by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/84
• Remove publishDir from config files, rely on workflow.output by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/85
• Refactor: use nf-core-utils plugin instead of nf-core utils subworkflows by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/88
• Release v1.0.0 by @ramprasadn in https://github.com/nf-core/createpanelrefs/pull/46

New Contributors

• @maxulysse made their first contribution in https://github.com/nf-core/createpanelrefs/pull/5
• @ramprasadn made their first contribution in https://github.com/nf-core/createpanelrefs/pull/9
• @lescai made their first contribution in https://github.com/nf-core/createpanelrefs/pull/13
• @nf-core-bot made their first contribution in https://github.com/nf-core/createpanelrefs/pull/18
• @jemten made their first contribution in https://github.com/nf-core/createpanelrefs/pull/28
• @danielhmendoza01 made their first contribution in https://github.com/nf-core/createpanelrefs/pull/56
• @fellen31 made their first contribution in https://github.com/nf-core/createpanelrefs/pull/66
• @Copilot made their first contribution in https://github.com/nf-core/createpanelrefs/pull/82

Full Changelog: https://github.com/nf-core/createpanelrefs/commits/1.0.0