---

name: workflow-authoring description: "Write, refactor, and troubleshoot Snakemake 9.23.1 Snakefiles, rules, wildcards, modules, checkpoints, includes, and script/notebook/wrapper/CWL hooks." disable-model-invocation: true metadata: disco-role: operating license: MIT

Workflow Authoring

Use this sub-skill when the task is about Snakefile language semantics or DAG construction: rules, wildcards, directives, helper functions, expand(), glob_wildcards(), multiext(), output flags, includes, modules, checkpoints, scripts, notebooks, wrappers, CWL hooks, and authoring-time validation.

Route by Task

• Rule syntax or helper APIs: read references/language-reference.md for Snakemake 9.23.1 rule anatomy, wildcard behavior, input functions, shell formatting, output flags, and hook directives.
• Refactoring workflow structure: read references/workflow-patterns.md for safe patterns around named IO, reusable rule files, modules, checkpoints, ambiguity reduction, and script extraction.
• Authoring errors: read references/troubleshooting.md for parser/syntax errors, wildcard ambiguity, MissingInputException, InputFunctionException, checkpoint misuse, module surprises, optional script/notebook dependencies, and stale --reason commands.
• Starter example: run python scripts/minimal_snakefile.py --help or generate a tiny isolated workflow with python scripts/minimal_snakefile.py --output-dir demo-workflow.

Boundaries

• Use ../configuration-data/SKILL.md for config files, schemas, tabular metadata, PEP/sample sheets, and validation policy beyond simple Snakefile reads.
• Use ../execution-cli/SKILL.md for CLI flags, profiles, targets, scheduling, resources at execution time, and dry-run strategy beyond authoring smoke checks.
• Use ../deployment-storage/SKILL.md for conda, containers, wrappers with environment setup, storage plugins, and remote provider credentials.
• Use ../debugging-reporting/SKILL.md for lint/report/test artifacts, CI, generated reports, benchmark outputs, and deep runtime debugging.
• Use ../python-api-plugins/SKILL.md for programmatic execution through Snakemake Python APIs or plugin development.

Default Authoring Validation

From the workflow directory, prefer a current Snakemake 9.23.1 loop:

snakemake --snakefile Snakefile --cores 1 --dry-run --printshellcmds
snakemake --snakefile Snakefile --cores 1 --dry-run --dag > dag.dot
python -m snakemake --help

Do not copy older commands that use --reason; Snakemake 9.23.1 does not accept that flag, although dry-run output still reports job reasons.