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Add pattern to input field #832

Merged
merged 3 commits into from
Feb 19, 2025
Merged

Add pattern to input field #832

merged 3 commits into from
Feb 19, 2025

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pinin4fjords
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@pinin4fjords pinin4fjords commented Feb 18, 2025 •
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Adding a pattern to the input field. Closes #831.

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/ampliseq branch on the nf-core/test-datasets repository.
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  • Output Documentation in docs/output.md is updated.
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@pinin4fjords pinin4fjords marked this pull request as draft February 18, 2025 10:23
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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.

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github-actions bot commented Feb 18, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d121b0d

+| ✅ 305 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • 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:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2025-02-19 09:47:51

@pinin4fjords pinin4fjords mentioned this pull request Feb 18, 2025
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@pinin4fjords pinin4fjords changed the title Update nextflow_schema.json to demo type issue Add pattern to input field Feb 18, 2025
@pinin4fjords pinin4fjords marked this pull request as ready for review February 18, 2025 10:35
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Thanks! However, that will prevent the current flexibility?

Path to sample sheet, either tab-separated (.tsv), comma-separated (.csv), or in YAML format (.yml/.yaml)

csv and yml/yaml will be not accepted then?

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pinin4fjords commented Feb 18, 2025 •
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Thanks! However, that will prevent the current flexibility?

Path to sample sheet, either tab-separated (.tsv), comma-separated (.csv), or in YAML format (.yml/.yaml)

csv and yml/yaml will be not accepted then?

Sorry, yes, you're right, I was too hasty.

The right fix is probably something flexible like this: https://github.com/nf-core/differentialabundance/blob/3dd360fed0dca1780db1bdf5dce85e5258fa2253/nextflow_schema.json#L35

There is currently a bug in Platform that will also prevent that working correctly with datasets, but that will be addressed in due course.

d4straub
d4straub reviewed Feb 18, 2025
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Require all parameters that point to files a pattern? Because there are a few more...

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pinin4fjords commented Feb 18, 2025 •
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Require all parameters that point to files a pattern? Because there are a few more...

If you want them to be pickable from datasets in Platform, yes.

d4straub
d4straub approved these changes Feb 19, 2025
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LGTM!

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Alright, we add that for input now and keep the issue open for now. The aim would be to add a pattern for all, or at least most, file inputs.

@d4straub d4straub merged commit 89336e1 into dev Feb 19, 2025
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