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Release v2.3.0 #666

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Release v2.3.0 #666

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ramprasadn
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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/raredisease branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

ramprasadn and others added 30 commits September 13, 2024 13:58
@ramprasadn
add mito
3af2b52
@ramprasadn
annotate
a87672e
@ramprasadn
bumpversion
6dacbb6
@ramprasadn
align mt reads to mt and not genome
505c2b8
@ramprasadn
Merge pull request #610 from nf-core/bumpversion230
695ccc3 
Bumpversion 2.2.0->2.3.0dev
@ramprasadn
Merge branch 'dev' of github.com:nf-core/raredisease into mito
1a48be1
@ramprasadn
update changelog
9575a7f
@ramprasadn
include filter
2bb4586
@ramprasadn
update usage docs
537de87
@ramprasadn
prettier
099a566
@ramprasadn
update docs
a57f931
@ramprasadn
lint
877cb31
@ramprasadn
Merge pull request #608 from nf-core/mito
c3aacee 
Add option to analyse only mitochondria
@ramprasadn
Merge branch 'dev' of github.com:nf-core/raredisease into bcftools-fi…
eb963ec 
…lter
@ramprasadn
changelog
c1ddf4c
@ramprasadn
fix declaration error
7d5e14e
@jemten
allow vep 112
2a505df
@jemten
prettier
1021df2
@ramprasadn
update docs
69eb6a1
@ramprasadn
lint
931fc00
@ramprasadn
Merge pull request #616 from nf-core/bcftools-filter
df4db70 
5% frequency threshold for mitochondrial clinical vcfs
@ramprasadn
update README
d509436
@ramprasadn
Merge branch 'dev' of github.com:nf-core/raredisease into dev
39e473d
@ramprasadn
update module
953316b
@jemten
remove enum on vep cache version
5e177a2
@jemten
Merge branch 'dev' into add_vep_112_option
e583e15
@ramprasadn
Merge pull request #617 from nf-core/add_vep_112_option
985230b 
allow vep 112
@ramprasadn
Merge branch 'dev' into updatetabixbgzip
63f36cf
@ramprasadn
Merge pull request #618 from nf-core/updatetabixbgzip
7da78ba 
Minor fixes
@ramprasadn
update modules
64bea68
rannick
rannick approved these changes Jan 22, 2025
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Fantastic!

CHANGELOG.md
@@ -3,6 +3,58 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## 2.3.0 - Getafix [xxxx-xx-xx]
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Don't forget to update with the date

CHANGELOG.md Outdated Show resolved Hide resolved
conf/modules/annotate_genome_snvs.config Show resolved Hide resolved
docs/usage.md Outdated Show resolved Hide resolved
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rannick commented Jan 22, 2025

And avoiding file extension in the prefixes, but can be done later

ramprasadn and others added 19 commits January 22, 2025 11:18
@ramprasadn
Annick's review suggestions
9864840
@ramprasadn
prettier
6dfb6f1
@ramprasadn
Merge pull request #669 from nf-core/ramPR
565ef54 
Review suggestions on v2.3.0
@nf-core-bot
Template update for nf-core/tools version 3.2.0
6e6352e
@ramprasadn
Merge remote-tracking branch 'origin/nf-core-template-merge-3.2.0' in…
c9680fb 
…to sync320
@ramprasadn
fix lint
d981bb2
@ramprasadn
Merge pull request #671 from nf-core/sync320
610308e 
Template update v320
@ramprasadn
update haplogrep3
e218bd3
@ramprasadn
fix lint
48705d2
@ramprasadn
update path
f4da377
@ramprasadn
Merge pull request #672 from nf-core/haplogrep3
7f0de75 
update haplogrep3
@ramprasadn
Keep only SVs that PASS
cb2c7a6
@ramprasadn
fix for wes
f1c4ced
@ramprasadn
review suggestions
f2038cd
@ramprasadn
Merge pull request #673 from nf-core/filtersvcalls
4a1fca0 
Keep only SVs that PASS the filter
@ramprasadn
report retroseq version
f151e50
@ramprasadn
add version mitodel
058b7a7
@ramprasadn
modify versions
9c3cc2a
@ramprasadn
Merge pull request #674 from nf-core/versions
055ddf8 
Update versions
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@ramprasadn @rannick @jemten @nf-core-bot @peterpru @fevac