v2.1.2

2.1.2

New Commands

• bactopia-scaffold - scaffold Bactopia components (modules, subworkflows, workflows) from bioconda/conda-forge packages with subcommands: lookup, test-data, module, subworkflow, tool

New Lint Rules

• W021 - Workflow params block: Value<Path> / Value<Path?> wrappers must be replaced with bare Path / Path? (FAIL)
• S025 - Subworkflow take: block: Value<Path> / Value<Path?> wrappers must be replaced with bare Path / Path? (FAIL)
• S026 - All emit channels must have a corresponding @output tag (FAIL/WARN)
• S027 - @output field descriptions must not exist for channel.empty() emits (FAIL)

Bug Fixes

• Fixed _infer_scope classifying run-scope subworkflows as sample scope when sample_outputs was declared but empty
• Fixed _extract_tool_info returning build hash as version for conda specs with build strings (e.g., midas=1.3.2=pyh7cba7a3_7)
• Hardcoded merlin subworkflow as sample scope (dynamic dispatcher with no fixed output fields)

Enhancements

• bactopia-lint gains --subworkflow and --workflow filter options to complement existing --module
• Lint runner now supports subworkflow_filter and workflow_filter for fine-grained single-component linting
• Extracted shared bactopia.conda module for Anaconda API queries (bioconda/conda-forge version lookup, container ref construction, component existence checking); refactored bactopia-update to use it
• bactopia-catalog improved scope inference and tool info extraction
• Workflow param parser now captures type annotations (e.g., String, Value<Path>)
• Subworkflow take: block inputs are now parsed with name, type, and line number
• GroovyDoc parser now tracks per-@output field presence (doc_output_has_fields)
• Structure parser now detects channel.empty() emit channels (empty_emit_channels)