AgentSkillsCN

pipeline-check

运行Snakemake语法检查、干运行验证以及R语言的语法检查，以验证流水线变更。

SKILL.md
--- frontmatter
name: pipeline-check
description: Run Snakemake linting, dry-run validation, and R linting to validate pipeline changes
disable-model-invocation: true

Pipeline Check

Run the full pipeline validation suite to catch issues before committing.

Steps

  1. •Snakemake lint: Run micromamba run -n q100-smk snakemake --lint to check for rule issues
  2. •Snakemake dry-run: Run micromamba run -n q100-smk snakemake -n -- all to verify the DAG resolves
  3. •Snakefmt check: Run micromamba run -n q100-smk snakefmt --check workflow/ to verify Snakemake formatting
  4. •R lint: Run Rscript -e 'lintr::lint_dir("R/")' to check R code quality
  5. •Markdownlint: Run markdownlint '**/*.md' --ignore node_modules to check markdown files

Report results clearly, grouping errors by category (lint, dry-run, format, R, markdown). If everything passes, confirm all checks passed.