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Fix overzealous schema errors when only a single param does not pass#858

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jfy133 merged 6 commits intodevfrom
fix-overzealous-schemaerrors
Sep 5, 2025
Merged

Fix overzealous schema errors when only a single param does not pass#858
jfy133 merged 6 commits intodevfrom
fix-overzealous-schemaerrors

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@jfy133 jfy133 commented Sep 5, 2025 •
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To close #836

And add a HiRSE badge for promotion of the pipleine in GErman circles

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).

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github-actions Bot commented Sep 5, 2025

This PR is against the main branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @jfy133,

It looks like this pull-request is has been made against the nf-core/mag main branch.
The main branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to main are only allowed if they come from the nf-core/mag dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@jfy133 jfy133 changed the base branch from main to dev September 5, 2025 08:04
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github-actions Bot commented Sep 5, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 44c49d3

+| ✅ 363 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 nextflow.config: Specify any additional parameters here
  • 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!

❔ 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 2025-09-05 08:55:24

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jfy133 commented Sep 5, 2025

@nf-core-bot fix linting

@jfy133 jfy133 merged commit 6e229be into dev Sep 5, 2025
14 checks passed
@jfy133 jfy133 deleted the fix-overzealous-schemaerrors branch September 5, 2025 09:41
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@maxulysse maxulysse maxulysse approved these changes

@nvnieuwk nvnieuwk nvnieuwk approved these changes

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

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

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parameters error in nanopore only assembly in dev

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@jfy133 @maxulysse @nvnieuwk