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Fix faulty HQ nanopore key name in long-read assembly mode condition#885

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jfy133 merged 2 commits intodevfrom
fix-883
Oct 17, 2025
Merged

Fix faulty HQ nanopore key name in long-read assembly mode condition#885
jfy133 merged 2 commits intodevfrom
fix-883

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@jfy133 jfy133 commented Oct 17, 2025 •
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Fixes #883 by using the right keyname in the conditions for both FL and METAmdbg

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).

@jfy133 jfy133 linked an issue Oct 17, 2025 that may be closed by this pull request
unknown lr_platform provided to Flye #883
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jfy133 commented Oct 17, 2025
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nf-core-bot commented Oct 17, 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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github-actions Bot commented Oct 17, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8e4fa38

+| ✅ 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 3.3.2
  • Run at 2025-10-17 08:27:22

@jfy133 jfy133 merged commit 4703a65 into dev Oct 17, 2025
22 checks passed
@jfy133 jfy133 deleted the fix-883 branch October 17, 2025 10:56
@jfy133 jfy133 mentioned this pull request Oct 25, 2025
Merged
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@dialvarezs dialvarezs dialvarezs approved these changes

@d4straub d4straub Awaiting requested review from d4straub d4straub is a code owner

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

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

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unknown lr_platform provided to Flye

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