update schema - #101
update schema#101
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🟡 Changes recommended
The updated schema contains multiple verified JSON Schema type/default mismatches (and one incorrect regex) that will cause validation/UI issues unless corrected.
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Pull request overview
This PR updates nextflow_schema.json, which defines and documents the Nextflow pipeline parameters (and is used by nf-schema-based tooling for validation/UI).
Changes:
- Reformats and substantially expands the JSON schema structure (
$defs,allOf, and a large top-levelpropertiesblock). - Adds/updates defaults for multiple parameters (e.g., container image, project naming, AIRR/template paths, clustering options).
- Introduces many additional single-cell and analysis parameters to the schema surface.
File summaries
| File | Description |
|---|---|
| nextflow_schema.json | Large schema refactor/expansion to document and validate pipeline parameters and defaults. |
Review details
Suppressed comments (2)
nextflow_schema.json:228
simulation_depthis declared as a string but the default is a number; this is a schema type mismatch and differs fromnextflow.configwhere it is a quoted string. Quote the default value.
"simulation_depth": {
"type": "string",
"default": 1000
},
nextflow_schema.json:232
kmer_min_depthis declared as a string but the default is a number; this is a schema type mismatch and differs fromnextflow.configwhere it is a quoted string. Quote the default value.
"kmer_min_depth": {
"type": "string",
"default": 3
},
- Files reviewed: 1/1 changed files
- Comments generated: 5
- Review effort level: Lite
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Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
|
@copilot resolve the merge conflicts in this pull request |
# Conflicts: # nextflow_schema.json Co-authored-by: dimalvovs <1246862+dimalvovs@users.noreply.github.com>
Resolved the merge conflicts with |
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