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Fix broken schema references preventing Seqera Platform launch #30

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Merged
adamjtaylor merged 11 commits into from
Jan 15, 2026
Merged

Fix broken schema references preventing Seqera Platform launch #30

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5da3eed
Initial plan
Copilot Jan 15, 2026
837e118
Fix nextflow_schema.json structure: rename definition, add synapsecon…
Copilot Jan 15, 2026
33c301c
Add description for n_components parameter
Copilot Jan 15, 2026
f029928
Remove synapseconfig parameter as requested
Copilot Jan 15, 2026
aeb7db1
Fix spelling errors in parameter descriptions
Copilot Jan 15, 2026
40ffa9b
Initial plan
Copilot Jan 15, 2026
d8bf72f
Add optional save_ometiff parameter and publishDir to bioformats2ometiff
Copilot Jan 15, 2026
666b8a7
Update modules/bioformats2ometiff.nf
adamjtaylor Jan 15, 2026
efaa233
Move publishDir after output block and fix schema typo
Copilot Jan 15, 2026
7990d3c
Merge pull request #33 from Sage-Bionetworks-Workflows/copilot/add-op…
adamjtaylor Jan 15, 2026
edf6cf0
Merge branch 'zp' into copilot/fix-broken-schema-references
adamjtaylor Jan 15, 2026
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13 changes: 6 additions & 7 deletions nextflow_schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@
}
}
},
"miniatue_options": {
"miniature_options": {
"title": "Miniature options",
"type": "object",
"fa_icon": "fas fa-palette",
Expand All @@ -38,7 +38,7 @@
},
"level": {
"type": "integer",
"description": "The pyramid level used in thumbnauls, Default: -1 (smallest)",
"description": "The pyramid level used in thumbnails, Default: -1 (smallest)",
"default": -1
},
"dimred": {
Expand All @@ -49,22 +49,21 @@
},
"colormap": {
"type": "string",
"description": "The colormap used. Ensure colormap is compatiable with `n_components` selected ",
"description": "The colormap used. Ensure colormap is compatible with `n_components` selected ",
"enum": ["UCIE", "LAB", "RGB", "BREMM", "SCHUMANN", "STEIGER", "TEULING2", "ZIEGLER","CUBEDIAGONAL"],
"default": "UCIE"
},
"n_components": {
"type": "integer",
"description": "",
"description": "Number of components for dimensionality reduction",
"default": 3,
"enum": [2,3]
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/parameters"
}
{ "$ref": "#/definitions/input_output_options" },
{ "$ref": "#/definitions/miniature_options" }
]
}