Fall back to nextflow_schema.json types for CLI param coercion#7108
Fall back to nextflow_schema.json types for CLI param coercion#7108ewels wants to merge 1 commit intonextflow-io:masterfrom
nextflow_schema.json types for CLI param coercion#7108Conversation
Under syntax parser v2, CLI params arrive as strings unless the pipeline declares typed params in main.nf or non-null defaults in nextflow.config. This breaks pipelines moving to v26.04.0 that rely on type-coerced params (e.g. numeric comparisons on `params.max_cpus`). When a `nextflow_schema.json` lives next to main.nf, read property types from it and coerce CLI string values before they reach ConfigBuilder. Coercion is best-effort: missing or malformed schemas are ignored, and values that don't match a declared type are left untouched. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> Signed-off-by: Phil Ewels <phil.ewels@seqera.io>
✅ Deploy Preview for nextflow-docs-staging canceled.
|
ewels
changed the title
nextflow_schema.json types for CLI param coercion
Note: duplication with the language serverNote that the Nextflow language server already has equivalent schema-walking code:
The right consolidation is to lift the schema-walking into the shared
Both repos would agree on what counts as a property and which keys the schema is searched under. If you like, I can re-shape this PR to put the schema reader in |
| static Map<String,String> readSchemaTypes(Path schemaFile) { | ||
| try { | ||
| final root = new JsonSlurper().parse(schemaFile) | ||
| final types = new LinkedHashMap<String,String>() |
There was a problem hiding this comment.
The types keyword can also be a list of multiple types, how would you handle that case?
2 participants
Summary
Under syntax parser v2 (default in 26.04.0), CLI params arrive as strings. Unless the pipeline declares typed params in
main.nfor non-nulldefaults innextflow.config, those values stay as strings — which breaks param logic that expects e.g. numeric comparison onparams.max_cpus.This change reads property types from
nextflow_schema.json(the nf-core convention) when it sits next tomain.nf, and uses them to coerce CLI string values before they reachConfigBuilder. Pipelines that already had a schema get typed params for free with nomain.nfchanges.nextflow.config.SchemaParamsHelperCmdRun.run(), immediately afterparsedParams()propertiesblocks at the top level and underdefinitions/\$defs/allOf/oneOf/anyOfstring/integer/number/boolean(anything else left untouched)NF.isSyntaxParserV2()and respectsNXF_DISABLE_PARAMS_TYPE_DETECTIONparams { }in main.nfParamsDslTest plan
SchemaParamsHelper(12 cases: flat schema, nesteddefinitions/\$defs/allOf, coercion of all four JSON Schema types, malformed schema, missing schema, mixed-case booleans, duplicate-name first-wins,NXF_DISABLE_PARAMS_TYPE_DETECTIONopt-out, syntax parser v1 opt-out, pre-typed values from params files, typeless property)nextflow_schema.jsonconfirms--max_cpus 8 --skip_qc TRUE --ratio 0.5arrive asInteger/Boolean/FloatCmdRunTest,ParamsDslTest, and config parser v2 tests still pass🤖 Generated with Claude Code