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Bump bcftools to 1.25 - #13480

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bump/bcftools-1.25
Oct 28, 2026
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Bump bcftools to 1.25#13480
matthdsm merged 22 commits into
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bump/bcftools-1.25

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@matthdsm matthdsm commented Oct 28, 2026 •
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Updated bcftools/htslib to v1.25
Updated htslib/* to v1.25
Updated some tests to use nft-utils along the way

PR checklist

Closes #XXX

  • 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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Broadcast software version numbers to topic: versions - See version_topics
  • Follow the naming conventions.
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  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@matthdsm
matthdsm requested a review from maxulysse as a code owner October 28, 2026 09:56
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This PR exceeds the recommended size of 1000 lines. Please make sure you are NOT addressing multiple issues with one PR. Note this PR might be rejected due to its size.

jfy133 and others added 9 commits October 28, 2026 11:02
@jfy133 @matthdsm
Add license header text to all modules and subworkflow main.nf files (#…
df23e04 
…13448)

* Add header to all subworkflows

* Add two subworkflow stragglers

* Add all license header to all module main.nf files

* Add 33 moduel stragglers

* [skip ci] remove trailing space end of first line of license header

---------

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
@awgymer @matthdsm
fix: remove nextflow shebang lines which break lint (#13472)
3605fba 
* fix: remove nextflow shebang lines which break lint

* test: regenerate tinc stub snapshot for nft-utils 1.x key order
@bounlu @matthdsm
fix typo (#13470)
2d86750
@matthdsm
Use environment variables for test data base paths (#13474)
db1a357 
## Feat
Add optional env variables for test data base paths so devs can set it to a local path without running the risk of committing changes that shouldn't be there.

## Reason
I did exactly that and want to add the env variable to my `.bashrc`. No more timeouts from github and faster tests!
@DylanMHouse @vagkaratzas
@awgymer @matthdsm
new module: longphase/modcall (#13388)
101eaa4 
* Add longphase/modcall module

* New module: longphase/modcall

* Update modules/nf-core/longphase/modcall/main.nf

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>

* Update modules/nf-core/longphase/modcall/meta.yml

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>

* Update modules/nf-core/longphase/modcall/meta.yml

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>

* Update modules/nf-core/longphase/modcall/tests/main.nf.test

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>

* Update modules/nf-core/longphase/modcall/tests/main.nf.test

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>

* Update modules/nf-core/longphase/modcall/tests/main.nf.test

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>

* Update modules/nf-core/longphase/modcall/tests/main.nf.test

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>

* Update modules/nf-core/longphase/modcall/tests/main.nf.test

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>

* Update modules/nf-core/longphase/modcall/meta.yml

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>

* Update modules/nf-core/longphase/modcall/meta.yml

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>

* Update modules/nf-core/longphase/modcall/meta.yml

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>

* Regenerated test with new conda to match update. Added EDAM tags for .bai. No valid EDAM tag for .fai. Linted module.

* Regenerated snapshot on cluster to run with minimum resource requirements

* Update modules/nf-core/longphase/modcall/main.nf

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>

* Update modules/nf-core/longphase/modcall/meta.yml

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>

* Update modules/nf-core/longphase/modcall/main.nf

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>

* regenerated snapshot

* fixed meta.yml with nf-core modules lint --fix

* lint again on main machine to prevent hooks from failing?

* Update modules/nf-core/longphase/modcall/main.nf

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>

* regenerated snap for the final time (I hope >:D)

---------

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>
Co-authored-by: awgymer <24782660+awgymer@users.noreply.github.com>
@matthdsm
align NXF_VER and NFT_VER across CI (#13477)
79cc2c2
@renovate @matthdsm
Update pre-commit hooks (#13479)
8870f02 
Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
@erikrikarddaniel @claude @matthdsm
Add raxmlng/evaluate: optimise branch lengths and model on a fixed tr…
32d9138 
…ee (#13475)

* Add raxmlng/evaluate: optimise branch lengths and model on a fixed tree

Runs raxml-ng --evaluate on an alignment, a tree and a model: the
topology is kept, only branch lengths and model parameters are
optimised. The seed defaults to 42 as in raxmlng/search. The
environment, container and conda lock files are the same as for
raxmlng/search.

Generated by Claude
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_014eSqkuYZXfNiWy87y3srup

* Add EDAM ontologies to the raxmlng/evaluate meta.yml

Alignment inputs are FASTA or PHYLIP, trees are Newick, and the model
and log files are textual.

Generated by Claude
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_014eSqkuYZXfNiWy87y3srup

---------

Co-authored-by: Claude Sonnet 5.5 <noreply@anthropic.com>
@erikrikarddaniel @claude @matthdsm
Add raxmlng/moose: RAxML-NG model selection without a tree search (#1…
f5e4617 
…3476)

* Add raxmlng/moose: RAxML-NG model selection without a tree search

Runs raxml-ng --moose on an alignment and returns the selected model
(*.raxml.moose.bestModel) and the log. The data type is an input, the
seed defaults to 42 as in raxmlng/search. The environment, container and
conda lock files are the same as for raxmlng/search.

Generated by Claude
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_014eSqkuYZXfNiWy87y3srup

* Add EDAM ontologies to the raxmlng/moose meta.yml

Alignment inputs are FASTA or PHYLIP, trees are Newick, and the model
and log files are textual.

Generated by Claude
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_014eSqkuYZXfNiWy87y3srup

---------

Co-authored-by: Claude Sonnet 5.5 <noreply@anthropic.com>
@matthdsm
matthdsm enabled auto-merge October 28, 2026 14:09
@matthdsm
matthdsm added this pull request to the merge queue Oct 28, 2026
@matthdsm
matthdsm removed this pull request from the merge queue due to a manual request Oct 28, 2026
@matthdsm

matthdsm commented Oct 28, 2026

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The merge queue seems very eager.... Tests are still running and the PR was already queued

@matthdsm
matthdsm added this pull request to the merge queue Oct 28, 2026
Merged via the queue into master with commit ed7a228 Oct 28, 2026
286 of 298 checks passed
@matthdsm
matthdsm deleted the bump/bcftools-1.25 branch October 28, 2026 15:10
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@maxulysse maxulysse maxulysse approved these changes
@pinin4fjords pinin4fjords Awaiting requested review from pinin4fjords
@edmundmiller edmundmiller Awaiting requested review from edmundmiller

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7 participants

@matthdsm @maxulysse @jfy133 @awgymer @bounlu @DylanMHouse @erikrikarddaniel