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name: configuration-data description: "Route Snakemake configuration, sample metadata, schema validation, pathvars, envvars, YTE, PEP, and data-driven helper tasks." disable-model-invocation: true metadata: disco-role: operating license: MIT

Configuration Data

Use this sub-skill when a Snakemake task involves configfile, CLI config overrides, profile-provided config, JSON/YAML config loading, config mutation, sample tables, snakemake.utils.validate, PEP metadata, envvars, pathvars, YTE-templated YAML, or data-driven helpers such as lookup, branch, evaluate, collect, subpath, and exists.

Route by Need

• Config sources, precedence, CLI quoting, profiles, YTE, envvars, pathvars, PEP, and helper patterns: read configuration-reference.md.
• JSON Schema validation for dictionaries, pandas tables, Polars tables, defaults, and relative $ref: read data-validation.md.
• Common failures and diagnostic signals for invalid config, schema errors, optional dependencies, pathvar cycles, and helper misuse: read troubleshooting.md.
• Standalone preflight for config/sample schemas before a full run: use validate_config_schema.py.

Fast Workflow

1. Inventory every config source: Snakefile configfile, included files, CLI --configfile, CLI --config, profiles, workflow profile, and any top-level Python update_config(config, ...).
2. Resolve precedence before editing rules: later config files recursively extend earlier files, --config wins over config files, and --replace-workflow-config discards workflow-defined config keys not provided by CLI config files.
3. Validate early, before rule definitions consume values: from snakemake.utils import validate; then validate(config, "schemas/config.schema.yaml") and validate any sample tables.
4. Keep secrets out of config files: assert names with envvars: and pass required values explicitly through params rather than assuming shell commands receive them.
5. Run snakemake --cores 1 --dry-run --printshellcmds after config/pathvar/schema changes. Do not add --reason; it is not a valid Snakemake 9.23.1 flag.

Boundaries

• Route rule graph syntax, wildcard design, module structure, and rule directives to ../workflow-authoring/SKILL.md; this sub-skill only owns the data/config semantics feeding them.
• Route command execution strategy, profile selection, cores, dry-runs, and executor flags to ../execution-cli/SKILL.md; this sub-skill covers only config-related CLI arguments.
• Route storage-provider setup to deployment/storage guidance; this sub-skill only notes that exists() respects Snakemake storage settings.
• Route report rendering and metadata display to debugging/reporting guidance unless the issue is config data feeding report metadata.