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Fix domain classification compatibility with long reads#929

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jfy133 merged 9 commits intodevfrom
928-fix-domain-classification-long-reads
Nov 13, 2025
Merged

Fix domain classification compatibility with long reads#929
jfy133 merged 9 commits intodevfrom
928-fix-domain-classification-long-reads

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@prototaxites prototaxites commented Nov 13, 2025 •
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Fixes #928

  • Remove the assembler argument from the script
  • Just try and pull out the identifier regardless of assembler

Also, I've changed the nf-test configuration so we trigger a full test run when a script in bin/ is modified. I think this is sensible, but happy to discuss if anyone disagrees.

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).

@prototaxites prototaxites changed the base branch from main to dev November 13, 2025 08:58
@nf-core nf-core deleted a comment from github-actions Bot Nov 13, 2025
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github-actions Bot commented Nov 13, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d37a552

+| ✅ 379 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   6 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • 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 nextflow.config: Specify any additional parameters here

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 3.4.1
  • Run at 2025-11-13 12:24:59

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prototaxites commented Nov 13, 2025

@nf-core-bot fix linting

@prototaxites prototaxites mentioned this pull request Nov 13, 2025
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jfy133
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LGTM, actually adding 'bin/*' to the nf-test trigger is a very good idea for all pipelines IMO - any chance you can copy the change to the tools repository too?

Comment thread CHANGELOG.md Outdated
jfy133
jfy133 reviewed Nov 13, 2025
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Comment thread CHANGELOG.md Outdated
@jfy133 jfy133 merged commit 52063e1 into dev Nov 13, 2025
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@jfy133 jfy133 deleted the 928-fix-domain-classification-long-reads branch November 13, 2025 13:07
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prototaxites commented Nov 13, 2025

I am ahead of you 😉

nf-core/tools#3897

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jfy133 commented Nov 13, 2025

I am ahead of you 😉

nf-core/tools#3897

Did I mention you are awesome?

@dialvarezs dialvarezs mentioned this pull request Dec 1, 2025
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@jfy133 jfy133 jfy133 approved these changes

@d4straub d4straub Awaiting requested review from d4straub d4straub 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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