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Patch nf schema - include integer & string as type for sample #450

Merged
merged 5 commits into from
Dec 12, 2024
Merged

Patch nf schema - include integer & string as type for sample #450

merged 5 commits into from
Dec 12, 2024

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Joon-Klaps
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PR checklist

Currently, nf-schema would throw a misleading error message if a sample name contained only digits:

-> Entry 2: Error for field 'sample' (303452): Sample name must be provided and cannot contain spaces

The newer version of nf-schema v2.2.1 throws both the validation error message as the set error message:
->Entry 2: Error for field 'sample' (303452): Value is [integer] but should be [string] (Sample name must be provided and cannot contain spaces)

Which is more clear. Additionally added that both strings and integers can be allowed as a type.

  • 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/viralrecon branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile 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).

@Joon-Klaps Joon-Klaps changed the title Patch nf schema Patch nf schema - include integer & string as type for sample Dec 12, 2024
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github-actions bot commented Dec 12, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d382134

+| ✅ 201 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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 base.config: Check the defaults for all processes
  • 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
  • system_exit - System.exit in nanopore.nf: System.exit(1) [line 246]

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-12-12 11:43:10

LilyAnderssonLee
LilyAnderssonLee approved these changes Dec 12, 2024
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LGTM!

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
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.

@Joon-Klaps Joon-Klaps merged commit 551cb49 into dev Dec 12, 2024
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@LilyAnderssonLee LilyAnderssonLee LilyAnderssonLee approved these changes

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