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Fix faulty YAML loading issue#986

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dialvarezs merged 7 commits intodevfrom
minimap2-yaml-issue
Mar 6, 2026
Merged

Fix faulty YAML loading issue#986
dialvarezs merged 7 commits intodevfrom
minimap2-yaml-issue

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@jfy133 jfy133 commented Mar 4, 2026 •
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Attempts to fix non-reproducible (on my machine), but reported by multiple user issue:

Error being reported, with bug being introduced in v5.4.0

ERROR ~ Could not find which method load() to invoke from this list:
  public java.lang.Object org.yaml.snakeyaml.Yaml#load(java.io.InputStream)
  public java.lang.Object org.yaml.snakeyaml.Yaml#load(java.io.Reader)
  public java.lang.Object org.yaml.snakeyaml.Yaml#load(java.lang.String)
  public java.lang.Object org.yaml.snakeyaml.Yaml#load(java.io.File)
  public java.lang.Object org.yaml.snakeyaml.Yaml#load(java.nio.file.Path)

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 marked this pull request as ready for review March 4, 2026 15:20
@github-actions github-actions bot added the size/m label Mar 4, 2026
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nf-core-bot commented Mar 4, 2026

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
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 Mar 4, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit cebc848

+| ✅ 383 tests passed       |+
#| ❔   1 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   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 nextflow.config: Specify any additional parameters here
  • 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!

❔ Tests ignored:

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

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-03-06 18:55:32

@dialvarezs dialvarezs merged commit ee6d96d into dev Mar 6, 2026
24 checks passed
@dialvarezs dialvarezs mentioned this pull request Mar 7, 2026
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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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