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Remove "None" definition from schema #851

Merged
merged 1 commit into from
Nov 17, 2022
Merged

Remove "None" definition from schema #851

merged 1 commit into from
Nov 17, 2022

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drpatelh
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Specifying "None" here in the schema breaks the config resolution on Tower meaning we are unable to use the pipeline from the Launchpad. The error that is generated is below:

If you use nf-core/sarek for your analysis please cite:
* The pipeline
  https://doi.org/10.12688/f1000research.16665.2
  https://doi.org/10.5281/zenodo.4468605
* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
  https://github.com/nf-core/sarek/blob/master/CITATIONS.md
-�[2m----------------------------------------------------�[0m-
Unable to read script: '/.nextflow/assets/nf-core/sarek/./workflows/sarek.nf' -- cause: /None

This was added in 6fd00e1 by @FriederikeHanssen ! Figuring this out has consumed my entire day 😅 You're welcome!

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github-actions bot commented Nov 17, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ba359ba

+| ✅ 151 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • schema_description - No description provided in schema for parameter: cnvkit_reference

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.6
  • Run at 2022-11-17 14:24:48

@maxulysse
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I think @asp8200 actually encountered some schema building issue when adding a params.
@asp8200 can you remind me what it was?

@FriederikeHanssen
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I am sorry

@drpatelh
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That's ok! All of the full-sized tests are running out-of-the-box now so I owed you one!

@asp8200
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asp8200 commented Nov 17, 2022 •
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I think @asp8200 actually encountered some schema building issue when adding a params. @asp8200 can you remind me what it was?

Yeah, I ran nf-core schema build and that changed a "default": null was also changed to "default": "None"

image

(But I didn't commit that change to dev or master)

@maxulysse
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ok, so given what @asp8200 just said, I think we need to fix tools and the schema so that no "None" definition are there.
So not your fault @FriederikeHanssen

@maxulysse maxulysse mentioned this pull request Nov 17, 2022
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@maxulysse maxulysse merged commit c22bd34 into dev Nov 17, 2022
@maxulysse maxulysse deleted the rm_none branch November 17, 2022 14:37
@pditommaso
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Holy crap, why it was happening only on Tower

@ewels
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ewels commented Nov 17, 2022

Holy crap, why it was happening only on Tower

I guess because the launchpad sends through all params from the form - including the default values supplied by the schema.

This is different behaviour to running the pipeline alone (quick launch or local). It's also different to the nf-core launch tools (web, cli), which only pass on values from the schema which have been changed from the default.

@ewels
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ewels commented Nov 17, 2022

Does this make sense? Makes perfect sense in my head but I'm not sure that I explained it very well 😆 Can try again if anyone is confused ☝🏻

@pditommaso
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Likely. It would be nice to have a snippet to replicate the error so that the error message can be better handled by nextflow

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@maxulysse maxulysse maxulysse approved these changes

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6 participants
@drpatelh @maxulysse @FriederikeHanssen @asp8200 @pditommaso @ewels