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Add metabuli/build module#8148

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sofstam merged 41 commits intomasterfrom
metabuli_build
Mar 13, 2026
Merged

Add metabuli/build module#8148
sofstam merged 41 commits intomasterfrom
metabuli_build

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@pawelciurkaardigen
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@pawelciurkaardigen pawelciurkaardigen commented Mar 27, 2025

PR checklist

Adds metabuli/build module that wraps metabuli build. Immediate need is having a possibility to use it in nf-core/createtaxdb to later use metabuli classify in nf-core/taxprofiler

Closes #8014

  • 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.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • 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

@pawelciurkaardigen pawelciurkaardigen marked this pull request as draft April 17, 2025 08:30
@jfy133 jfy133 marked this pull request as ready for review April 17, 2025 10:09
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@SPPearce SPPearce left a comment

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Any plan to finish this off @pawelciurkaardigen ? Looks like it isn't too far off.
Would swapping to emit a topics channel rather than the versions.yml

@pawelciurkaardigen
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Any plan to finish this off @pawelciurkaardigen ? Looks like it isn't too far off. Would swapping to emit a topics channel rather than the versions.yml

Hi @SPPearce that's something I have in my mind for a long time :) Let me try to move this forward during a span of next two weeks.

Is topics channel a replacement for versions.yml? I might not be super up to date with nf-core news :)

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Yep, basically instead of generating the versions.yml you just capture the version information via an eval in the output block.
Tutorial is here:
https://nf-co.re/docs/tutorials/migrate_to_topics/update_modules

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sofstam commented Mar 12, 2026

@nf-core-bot fix linting

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These are minor things, everyhting els ethe module looks good to me

@sofstam sofstam enabled auto-merge March 13, 2026 12:13
@sofstam sofstam added this pull request to the merge queue Mar 13, 2026
Merged via the queue into master with commit 5939738 Mar 13, 2026
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@sofstam sofstam deleted the metabuli_build branch March 13, 2026 12:18
DogaTestere pushed a commit to DogaTestere/modules that referenced this pull request Mar 13, 2026
* add metabuli/build module

* add test for metabuli/build

* tests

* update tests: pass accession2taxid from `prokaryotypes` directory, update snapshot to exclude md5 comparison of db.parameters

* tackling some linting errors

* filling in meta.yml

* don't validate split file for md5

* remove whitespaces

* address few code review comments

* replace realpath -s with echo as -s is not available in busybox image

* populate stub section with output databse files

* populate stub section with output databse files

* Added a test with two input assemblies, updated fasta input description

* add --cds-info input handling

* add --cds-info input handling

* Apply suggestion from @jfy133

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/nf-core/metabuli/build/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Add topics

* Update tests

* Fix linting

* Fix stub test

* Update snapshots

* Update modules/nf-core/metabuli/build/meta.yml

Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be>

* Fix linting

* Fix linting

---------

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
Co-authored-by: Sofia Stamouli <sstamo@login1.hsn.dardel.pdc.kth.se>
Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be>
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new module: metabuli/build

5 participants