nf-core/createpanelrefs
Generate Panel of Normals, models or other similar references from lots of samples
Version history
What’s Changed
- zenodo DOI by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/89
- Back to dev by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/90
- Add AGENTS.md file with nf-core agent instructions by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/91
- Remove vulnerable PR-comment artifact pattern by @mashehu in https://github.com/nf-core/createpanelrefs/pull/93
- Important! Template update for nf-core/tools v4.0.3 by @nf-core-bot in https://github.com/nf-core/createpanelrefs/pull/92
- Switch fix-linting to the hardened nf-core/actions reusable workflow by @mashehu in https://github.com/nf-core/createpanelrefs/pull/97
- Move seqeralabs/action-tower-launch to @v2 (v2.4.0) by @mashehu in https://github.com/nf-core/createpanelrefs/pull/98
- Important! Template update for nf-core/tools v4.1.0 by @nf-core-bot in https://github.com/nf-core/createpanelrefs/pull/95
- Important! Template update for nf-core/tools v4.1.0 by @nf-core-bot in https://github.com/nf-core/createpanelrefs/pull/96
- Important! Template update for nf-core/tools v4.2.1 by @nf-core-bot in https://github.com/nf-core/createpanelrefs/pull/99
- Update all modules by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/100
- Prepare release 1.1.0 by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/101
- Add metro map made with nf-metro by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/102
- Add –cnvkit_method to set the CNVkit batch sequencing method by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/103
- Add –cnvkit_annotate to label CNVkit target regions with gene names by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/104
- Add –gens_mosdepth_fast_mode to toggle mosdepth –fast-mode for long-read GENS PoN by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/105
- Format pipeline Nextflow code and configs with nextflow lint -format by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/106
- Update nf-core-utils to 0.7.0 and pin nf-schema in AWS full test by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/107
- Address 1.1.0 release review by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/110
- Drop nallo mention from –gens_mosdepth_fast_mode docs by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/109
- Run GENS tests as the calling user instead of root by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/111
- Fix GENS tests on CI: mount passwd and group for GATK4_CREATEREADCOUNTPANELOFNORMALS by @maxulysse in https://github.com/nf-core/createpanelrefs/pull/112
New Contributors
- @mashehu made their first contribution in https://github.com/nf-core/createpanelrefs/pull/93
Full Changelog: https://github.com/nf-core/createpanelrefs/compare/1.0.0...1.1.0
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_nameusage 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
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