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ACTUAL Release 3.4 #1321

Merged
merged 307 commits into from
Nov 15, 2023
Merged

ACTUAL Release 3.4 #1321

merged 307 commits into from
Nov 15, 2023

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FriederikeHanssen
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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/sarek 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>).
  • 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).

asp8200 and others added 30 commits September 20, 2023 13:00
@asp8200
Adding test of Sentieon VQSR not running for Sentieon DnaScope
5cb89c1
@asp8200
prettier
45e961a
@asp8200
Adding info concerning DNAscope. Also other minor improvements to the…
c1c7c6e 
… docs.
@asp8200
Removing redundant test
cfeb762
@SPPearce
Add NGSCheckMate
94ca07d
@SPPearce
Update CHANGELOG
21d38a2
@SPPearce
Update tools list for sampleqc
2e72d1c
@grantn5
adding some files for bcftools annotate
3cb5738
@SPPearce
Update CHANGELOG.md
cee8614
@SPPearce
Merge branch 'dev' into ngscheckmate
9c48c87
@SPPearce @maxulysse
Update conf/igenomes.config
a2496de 
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
@SPPearce @maxulysse
Update conf/igenomes.config
05f681e 
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
@SPPearce @maxulysse
Update CHANGELOG.md
9d9105c 
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
@SPPearce @maxulysse
Update conf/igenomes.config
2ab1e4d 
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
@SPPearce @maxulysse
Update conf/igenomes.config
ac649e0 
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
@SPPearce
Add tests, swap to ngscheckmate
a0e5f43
@SPPearce
Merge branch 'dev' into ngscheckmate
2c95984
@SPPearce
Fix NGSCheckMate test name
97e1fa6
@SPPearce
Merge remote-tracking branch 'refs/remotes/origin/ngscheckmate' into …
64273f3 
…ngscheckmate
@SPPearce
Update test
ad97096
@asp8200
Resolving merge conflict and renaming some sentieon subsections
9579af4
@SPPearce
Update output path and docs
7378fe9
@SPPearce
Change ngscheckmate publishdir
d37c24e
@SPPearce @maxulysse
Update tests/config/tags.yml
4e73bdb 
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
@grantn5
bcfannotate working with tests
76beace
@grantn5
updating documentations
58d22f7
@asp8200
Trying to sort out section and subsection for Sentieon/haplotyper and…
31fc80a 
… Sentieon/haplotyper/joint_germline
@maxulysse
back to dev
c2bb567
@maxulysse
Merge pull request #1271 from maxulysse/3.4dev
e69a301 
CHORES: Back to dev
@asp8200
Merge branch 'dev' into sentieon_dnascope
46f0788
@maxulysse
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Just waiting on #1325

@maxulysse
Merge pull request #1325 from nf-core/config_update
51c7676 
Update config files and other minor code polishing
maxulysse
maxulysse reviewed Nov 10, 2023
View reviewed changes
CHANGELOG.md Outdated Show resolved Hide resolved
FriederikeHanssen and others added 17 commits November 14, 2023 08:29
@FriederikeHanssen
Update all modules to have environment name
7fbbe46
@FriederikeHanssen
Update Changelog
0bfcf6f
@maxulysse
add icons + fix link
0834131
@maxulysse
fix link
02ef5c5
@maxulysse
update CHANGELOG
a2db8d0
@maxulysse
Merge pull request #1328 from maxulysse/docs
9b82f0c 
Fix links to docs
@FriederikeHanssen
update more modules
fd69216
@FriederikeHanssen
test everything
2e42d1b
@FriederikeHanssen
fix link
3651165
@FriederikeHanssen
I overdid the seach & replace
bffb445
@FriederikeHanssen
Exclude untar from nftest matrix
24eafe0
@FriederikeHanssen
Merge pull request #1327 from FriederikeHanssen/conda_env_name
ca7be8d 
Update all modules to have environment name
@FriederikeHanssen @maxulysse
Update CHANGELOG.md
d6e8958 
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
@FriederikeHanssen @maxulysse
Update conf/modules/annotate.config
4f0cc6d 
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
@FriederikeHanssen
Add SnpEff to full sized tests
0d36a50
@FriederikeHanssen
Merge branch 'dev' into fix_fulltest
c46c354
@FriederikeHanssen
Merge pull request #1330 from FriederikeHanssen/fix_fulltest
38fe279 
Add SnpEff to full sized tests
@maxulysse
Update test_freebayes.yml
35b5d3b 
remove contains test that are not stable
@FriederikeHanssen FriederikeHanssen merged commit 6aeac92 into master Nov 15, 2023
108 checks passed
@maxulysse
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Finally

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Reviewers

@LaurenceKuhl LaurenceKuhl LaurenceKuhl approved these changes

@mirpedrol mirpedrol mirpedrol approved these changes

@maxulysse maxulysse maxulysse approved these changes

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