Fix broken schema references preventing Seqera Platform launch #30

Copilot · 2026-01-15T10:37:53Z

The nextflow_schema.json contained structural errors causing Seqera Platform to reject valid parameters with "One or more fields contain invalid values."

Changes

Fixed definition typo: miniatue_options → miniature_options
Fixed broken references: allOf section now correctly references existing definitions instead of non-existent #/definitions/parameters
Improved documentation: Added description for n_components parameter
Fixed spelling errors: Corrected "thumbnauls" → "thumbnails" and "compatiable" → "compatible" in parameter descriptions

Before/After

// Before: broken reference
"allOf": [
  { "$ref": "#/definitions/parameters" }  // Does not exist
]

// After: valid references
"allOf": [
  { "$ref": "#/definitions/input_output_options" },
  { "$ref": "#/definitions/miniature_options" }
]

Schema now validates correctly and renders all parameter groups in the Seqera Platform launch form.

Original prompt

This section details on the original issue you should resolve

<issue_title>Broken references in schema preventing launch</issue_title>
<issue_description>The current nextflow_schema.json contains structural errors that prevent the Seqera Platform (Nextflow Tower) from correctly parsing the launch form. This results in a generic validation error: "One or more fields contain invalid values," even when the provided parameters are correct.

Issues Identified

Broken Reference: The allOf block (responsible for rendering the UI groups) references #/definitions/parameters, which does not exist in the schema.

Typo in Definitions: The definition for miniature options is misspelled as "miniatue_options", which may cause mismatches in the pipeline logic.

Missing Parameter: The synapseconfig parameter is used in run configurations but is missing from the schema, preventing it from appearing in the launch UI.

Proposed Fix

- Rename "miniatue_options" to "miniature_options".

- Add a definition for synapseconfig.

- Update the allOf section at the bottom of the file to correctly reference the existing definition blocks:
"allOf": [
    { "$ref": "#/definitions/input_output_options" },
    { "$ref": "#/definitions/miniature_options" }
]
```</issue_description>

<agent_instructions>Fix the structure of nextflow_schema.json by:

Renaming the definition key "miniatue_options" to "miniature_options".

Updating the "allOf" section at the bottom to correctly reference #/definitions/input_output_options and #/definitions/miniature_options.

Adding a string parameter for "synapseconfig" inside the miniature options block.

Ensuring all property types (boolean for remove_bg, integer for level/n_components) and enums match the existing schema logic.</agent_instructions>

## Comments on the Issue (you are @copilot in this section)

<comments>
<comment_new><author>@adamjtaylor</author><body>
FYI @PanZiwei I think this is preventing launch. My guess is that the past Seqera Platform version was running an older version of nf-schema that didn't correctly surface the issues with the schema, which now a newer version is.</body></comment_new>
</comments>

Fixes Broken references in schema preventing launch #29

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…fig, fix allOf references Co-authored-by: adamjtaylor <[email protected]>

Co-authored-by: adamjtaylor <[email protected]>

adamjtaylor · 2026-01-15T10:48:25Z

@copilot nextflow_schema.json:61-65
Remnove this we dont need synapseconfig at all that wass a mistake

Co-authored-by: adamjtaylor <[email protected]>

Copilot · 2026-01-15T10:50:16Z

@copilot nextflow_schema.json:61-65
Remnove this we dont need synapseconfig at all that wass a mistake

Removed the synapseconfig parameter in commit f029928.

adamjtaylor

LGTM. Nice job @copilot

Copilot

Pull request overview

This PR fixes critical structural errors in nextflow_schema.json that were preventing the Seqera Platform from correctly parsing the pipeline launch form.

Changes:

Corrected the typo in the definition key from "miniatue_options" to "miniature_options"
Fixed broken schema references in the allOf section to point to existing definitions
Added a description for the n_components parameter

Comments suppressed due to low confidence (2)

nextflow_schema.json:41

Corrected spelling of 'thumbnauls' to 'thumbnails'.

                    "description": "The pyramid level used in thumbnauls, Default: -1 (smallest)",

nextflow_schema.json:52

Corrected spelling of 'compatiable' to 'compatible'.

                    "description": "The colormap used. Ensure colormap is compatiable with `n_components` selected ",

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adamjtaylor · 2026-01-15T10:54:25Z

@copilot we do need to fix

nextflow_schema.json:41

Corrected spelling of 'thumbnauls' to 'thumbnails'.
"description": "The pyramid level used in thumbnauls, Default: -1 (smallest)",
nextflow_schema.json:52

Corrected spelling of 'compatiable' to 'compatible'.
"description": "The colormap used. Ensure colormap is compatiable with n_components selected ",

Co-authored-by: adamjtaylor <[email protected]>

Copilot · 2026-01-15T10:56:04Z

@copilot we do need to fix

nextflow_schema.json:41
...

Fixed both spelling errors in commit aeb7db1:

"thumbnauls" → "thumbnails" (line 41)
"compatiable" → "compatible" (line 52)

adamjtaylor · 2026-01-15T11:15:29Z

Confirming that this unblocks launch on Seqera Platform Version 25.1.5_5197cfa as deployed at Sage as of today.

Co-authored-by: adamjtaylor <[email protected]>

Co-authored-by: Copilot <[email protected]>

Co-authored-by: adamjtaylor <[email protected]>

…tional-save-for-images Feature merge into branch to unblock rapidly

aditigopalan · 2026-01-15T20:22:24Z

is there documentation about how to use the dev environment?

Co-authored-by: adamjtaylor <[email protected]>

Initial plan

5da3eed

Copilot AI assigned Copilot and adamjtaylor Jan 15, 2026

Copilot started work on behalf of adamjtaylor January 15, 2026 10:38 View session

Copilot AI and others added 2 commits January 15, 2026 10:41

Fix nextflow_schema.json structure: rename definition, add synapsecon…

837e118

…fig, fix allOf references Co-authored-by: adamjtaylor <[email protected]>

Add description for n_components parameter

33c301c

Co-authored-by: adamjtaylor <[email protected]>

Copilot AI changed the title ~~[WIP] Fix broken references in schema preventing launch~~ Fix broken schema references preventing Seqera Platform launch Jan 15, 2026

Copilot AI requested a review from adamjtaylor January 15, 2026 10:44

Copilot finished work on behalf of adamjtaylor January 15, 2026 10:44

Copilot started work on behalf of adamjtaylor January 15, 2026 10:48 View session

Remove synapseconfig parameter as requested

f029928

Co-authored-by: adamjtaylor <[email protected]>

adamjtaylor marked this pull request as ready for review January 15, 2026 10:50

adamjtaylor requested a review from Copilot January 15, 2026 10:50

adamjtaylor approved these changes Jan 15, 2026

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adamjtaylor requested a review from thomasyu888 January 15, 2026 10:51

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adamjtaylor self-requested a review January 15, 2026 10:54

Copilot started work on behalf of adamjtaylor January 15, 2026 10:54 View session

Fix spelling errors in parameter descriptions

aeb7db1

Co-authored-by: adamjtaylor <[email protected]>

Copilot finished work on behalf of adamjtaylor January 15, 2026 10:57

adamjtaylor approved these changes Jan 15, 2026

View reviewed changes

Copilot AI and others added 3 commits January 15, 2026 15:38

Initial plan

40ffa9b

Add optional save_ometiff parameter and publishDir to bioformats2ometiff

d8bf72f

Co-authored-by: adamjtaylor <[email protected]>

Update modules/bioformats2ometiff.nf

666b8a7

Co-authored-by: Copilot <[email protected]>

adamjtaylor mentioned this pull request Jan 15, 2026

Add optional publishDir for bioformats2ometiff converted images #32

Merged

9 tasks

Move publishDir after output block and fix schema typo

efaa233

Co-authored-by: adamjtaylor <[email protected]>

adamjtaylor requested review from aditigopalan and removed request for thomasyu888 January 15, 2026 16:05

adamjtaylor added 2 commits January 15, 2026 20:09

Merge pull request #33 from Sage-Bionetworks-Workflows/copilot/add-op…

7990d3c

…tional-save-for-images Feature merge into branch to unblock rapidly

Merge branch 'zp' into copilot/fix-broken-schema-references

edf6cf0

aditigopalan approved these changes Jan 15, 2026

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Copilot AI added a commit that referenced this pull request Jan 15, 2026

Revert schema typo fix to avoid conflict with PR #30

343b299

Co-authored-by: adamjtaylor <[email protected]>

adamjtaylor merged commit 0c5b79e into main Jan 15, 2026
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