Json schema improvements by ShimiraOleg · Pull Request #692 · nf-core/raredisease

ShimiraOleg · 2025-03-25T14:16:13Z

PR checklist

nvnieuwk

Awesome job! Here are some comments

Can you also check the nextflow_schema.json file in the root of the repository?

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>

github-actions · 2025-03-25T14:39:32Z

This PR is against the `master` 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 @ShimiraOleg,

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

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>

…Oleg/raredisease into json-schema-improvements

nvnieuwk

Can you add the "exists": true keyword to parameters that are files that should exist?

nvnieuwk

Hi, here are some more comments :)

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>

ShimiraOleg · 2025-03-25T17:11:17Z

Hi, here are some more comments :)

Ok, I've applied the feedback

jen-reeve · 2025-03-25T22:03:25Z

Do you know why the tests seem to be failing? It looks like there is one test that fails on dev, so unrelated to this PR, but some new tests are failing, presumably due to changes in this PR.

nvnieuwk · 2025-03-26T08:39:08Z

Do you know why the tests seem to be failing? It looks like there is one test that fails on dev, so unrelated to this PR, but some new tests are failing, presumably due to changes in this PR.

I've added some comments that should solve most of these issues
@ShimiraOleg please run nextflow run main.nf -profile test,docker -stub before pushing the changes, that way you are sure that validation hasn't been broken due to your changes 😁

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>

ShimiraOleg · 2025-03-26T13:32:29Z

Do you know why the tests seem to be failing? It looks like there is one test that fails on dev, so unrelated to this PR, but some new tests are failing, presumably due to changes in this PR.

I've added some comments that should solve most of these issues @ShimiraOleg please run nextflow run main.nf -profile test,docker -stub before pushing the changes, that way you are sure that validation hasn't been broken due to your changes 😁

Applied the comments, now it's only failing the pre-commit,

Also when i run the nextflow run main.nf -profile test,docker -stub on the codespace, it triggers an error (My theory is that this pipeline data is to big for the space codespace has)

nvnieuwk · 2025-03-26T13:39:15Z

@nf-core-bot fix linting pretty please

nvnieuwk · 2025-03-26T13:46:20Z

Not sure what to do about that last issue you are having... @ramprasadn have you had space issues before using this pipeline?

ramprasadn · 2025-03-26T13:53:27Z

I haven't run into space issues since we introduced cleaning step in the CI workflow. Let's see if the current attempt works 👀

nvnieuwk

Good job!

Refactored shema_input.json

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nvnieuwk changed the base branch from master to dev March 25, 2025 14:21

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ShimiraOleg and others added 2 commits March 25, 2025 11:33

Update assets/schema_input.json

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Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>

Update assets/schema_input.json

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Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>

ShimiraOleg and others added 5 commits March 25, 2025 11:44

Update assets/schema_input.json

964675a

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>

Update assets/schema_input.json

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Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>

Update assets/schema_input.json

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Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>

Changed 'shema_input.json' and 'nextflow_schema.json' with corrections

42b8ff5

Merge branch 'json-schema-improvements' of https://github.com/Shimira…

235df3c

…Oleg/raredisease into json-schema-improvements

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ShimiraOleg and others added 2 commits March 25, 2025 13:39

Update nextflow_schema.json

98b1d3f

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>

Corrections on the 'nextflow_schema.json'

306f523

jen-reeve linked an issue Mar 25, 2025 that may be closed by this pull request

JSON schema: Raredisease #691

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nvnieuwk reviewed Mar 26, 2025

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nvnieuwk and others added 2 commits March 26, 2025 09:39

Merge branch 'dev' into json-schema-improvements

e252db0

Update nextflow_schema.json

e29886b

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>

Update nextflow_schema.json

e6c0651

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>

[automated] Fix code linting

0accfbd

ShimiraOleg requested a review from nvnieuwk March 26, 2025 14:12

nvnieuwk approved these changes Mar 26, 2025

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ShimiraOleg merged commit 35c7643 into nf-core:dev Mar 26, 2025

ShimiraOleg deleted the json-schema-improvements branch March 26, 2025 14:22

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ShimiraOleg commented Mar 25, 2025

PR checklist

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github-actions Bot commented Mar 25, 2025

This PR is against the master branch ❌

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ShimiraOleg commented Mar 25, 2025

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nvnieuwk commented Mar 26, 2025

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ShimiraOleg commented Mar 26, 2025

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ramprasadn commented Mar 26, 2025

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This PR is against the `master` branch ❌