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Release 3.5.0 #1750

Merged
merged 399 commits into from
Dec 12, 2024
Merged

Release 3.5.0 #1750

merged 399 commits into from
Dec 12, 2024

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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>).
  • 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).

maxulysse and others added 30 commits September 23, 2024 18:03
@maxulysse
exclude tests for diff
102ea37
@maxulysse
exclude tests because of missing dependency
8368eae
@maxulysse
add default values for new options
8c5e8e7
@maxulysse
fix usage
ac569b4
@maxulysse
typo
92e3907
@maxulysse
Update CHANGELOG.md
2dd70b9
@maxulysse
fix bcftools annotate usage
a2a1462
@maxulysse
Merge pull request #1656 from asp8200/modify_snpeff_cache_setup
a4f07f7 
Retire snpeff_genome
@maxulysse
Merge branch 'dev' into massive_conda_update
474a9da
@maxulysse
exclude tests because of missing dependency
73c9f0e
@maxulysse
Fix default value
782d0a9
@maxulysse
fix usage of GATK4_GENOTYPEGVCFS
1c02dfd
@maxulysse
fix expected content
d61d456
@maxulysse
exclude tests coming from modules
f939581
@maxulysse
fix usage
4e5adf4
@maxulysse
exclude tests coming from modules + use debug
2c4225a
@maxulysse
update CHANGELOG
240db8d
@maxulysse
properly update samtools
f148972
@maxulysse
fix expected filename
42d9e32
@nevinwu
Merge branch 'dev' into dev
4922d11
@nevinwu
Merge pull request #1653 from nevinwu/dev
4c664f4 
Updates sarek_subway
@maxulysse
use nft-utils
6c19405
@maxulysse
let's capture ALL paths
c1ab3de
@maxulysse
Merge pull request #1661 from maxulysse/pipeline_test
6e7655f 
add pipeline level tests
@maxulysse
relative path
7dfc927
@maxulysse
update CHANGELOG
2067cb0
@maxulysse
print warnings instead of erroring
2736aac
@maxulysse
no need to import
a0dc4fb
@maxulysse
no need to import
0aafe1b
@maxulysse
fix comments
900a6c7
@github-actions GitHub Actions
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github-actions bot commented Dec 10, 2024 •
edited
Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 39c0c8f

+| ✅ 217 tests passed       |+
#| ❔  11 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-12-11 17:47:05

@FriederikeHanssen
Merge pull request #1613 from lindenb/pl_goleft
5c6be78 
added indexcov : finding large INDEL using the BAI index
FriederikeHanssen and others added 5 commits December 11, 2024 08:16
@FriederikeHanssen
update figure
4fecc5f
@FriederikeHanssen
remove --max from dcs
5335877
@FriederikeHanssen
reduce png size
e75cf94
@FriederikeHanssen
Update CHANGELOG.md
c2fbec1
@maxulysse
Merge pull request #1752 from FriederikeHanssen/fullsize
cd59770 
<!--
# nf-core/sarek pull request

Many thanks for contributing to nf-core/sarek!

Please fill in the appropriate checklist below (delete whatever is not
relevant).
These are the most common things requested on pull requests (PRs).

Remember that PRs should be made against the dev branch, unless you're
preparing a pipeline release.

Learn more about contributing:
[CONTRIBUTING.md](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
-->

## 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](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/sarek _branch_ on the
[nf-core/test-datasets](https://github.com/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>`).
- [ ] 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).
matthdsm
matthdsm approved these changes Dec 11, 2024
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I trust you guys 😉

@FriederikeHanssen
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For some reason manta and strelka are very brittle on conda. Each time another test fails but never the same and only in conda

matthdsm
matthdsm approved these changes Dec 11, 2024
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Still looks good to me!

@FriederikeHanssen FriederikeHanssen merged commit 4e7f474 into master Dec 12, 2024
168 of 179 checks passed
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@matthdsm matthdsm matthdsm approved these changes

@maxulysse maxulysse maxulysse approved these changes

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