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Add binner COMEBin#875

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d4straub merged 11 commits intonf-core:devfrom
d4straub:add-binner-COMEBin
Oct 17, 2025
Merged

Add binner COMEBin#875
d4straub merged 11 commits intonf-core:devfrom
d4straub:add-binner-COMEBin

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@d4straub d4straub commented Oct 7, 2025 •
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Attempt to add COMEBin. Follows #874.

Issues:

  • doesnt run with any CI test dataset (but the module does succeed with -profile test_full and output looks fine to me)
  • runtime seems long: 1-7h per samples, while METABAT2_METABAT2 requires <1min, BINNING:MAXBIN2 a few minutes

As a comment:
ext.args = "-b 20" helps with test data, because default value fails with "-profile test" (100 passes that step) as in https://github.com/ziyewang/COMEBin/issues/4 but instead the binner fails later after: "[CheckM - analyze] Identifying marker genes in bins.", so it doesnt make it work all the way through.

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/mag branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines 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).

d4straub
d4straub commented Oct 15, 2025
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Comment thread modules/nf-core/comebin/runcomebin/main.nf Outdated
d4straub
d4straub commented Oct 15, 2025
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Comment thread modules/nf-core/comebin/runcomebin/main.nf Outdated
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nf-core-bot commented Oct 15, 2025

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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d4straub commented Oct 15, 2025

@nf-core-bot fix linting

@d4straub d4straub marked this pull request as ready for review October 15, 2025 14:29
prototaxites
prototaxites reviewed Oct 15, 2025
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Comment thread modules/nf-core/comebin/runcomebin/comebin-runcomebin.diff Outdated
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prototaxites commented Oct 15, 2025

added a GPU label but didnt test it.

This won't work as the container environment needs to have GPU-specific versions of PyTorch etc.. Would need a GPU-specific container for this to work.

prototaxites
prototaxites reviewed Oct 15, 2025
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Comment thread conf/test_assembly_input.config
skip_prokka = true
skip_gtdbtk = true
skip_concoct = false
skip_comebin = true
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Unfortunately COMEBin seems to require data of sufficient complexity to complete without failure... Hence why the module has a stub test only

prototaxites
prototaxites reviewed Oct 15, 2025
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Comment thread conf/modules.config
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d4straub commented Oct 16, 2025

@nf-core-bot fix linting

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d4straub commented Oct 16, 2025 •
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Done:

  • final confirmation that -profile test_full works fine as is -> fine
  • port back changes of the COMEBin module to nf-core/modules -> adjust COMEBin modules#9202
  • re-install module here -> done

@d4straub d4straub mentioned this pull request Oct 16, 2025
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@d4straub d4straub requested a review from prototaxites October 17, 2025 06:43
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prototaxites approved these changes Oct 17, 2025
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OK, looks good to me!

One last little (non-code) thing, we should create an issue to remind us to try and find some test data so that we can actually test the module!

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d4straub commented Oct 17, 2025

Thanks! Will open an issue!

@d4straub d4straub merged commit db30b0a into nf-core:dev Oct 17, 2025
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@d4straub d4straub deleted the add-binner-COMEBin branch October 17, 2025 07:05
@d4straub d4straub mentioned this pull request Oct 17, 2025
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@jfy133 jfy133 mentioned this pull request Oct 25, 2025
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@prototaxites prototaxites prototaxites approved these changes

@jfy133 jfy133 Awaiting requested review from jfy133 jfy133 is a code owner

@muabnezor muabnezor Awaiting requested review from muabnezor muabnezor is a code owner

@dialvarezs dialvarezs Awaiting requested review from dialvarezs dialvarezs is a code owner

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