qmd-runner
Skill10 starsChanged 45 days agoNo licenceView on GitHub
Use when debugging Quarto (`.qmd`) notebooks chunk-by-chunk via auto-generated tryCatch runners. Triggers when a `quarto render` fails opaquely, when you need to surface every failing chunk in one pass rather than stop at the first error, when iteratively fixing analysis pipelines (Seurat / Bioconductor / GSEA / biomaRt / msigdbr / clusterProfiler), or when adopting an inherited notebook tree whose chunks no longer execute end-to-end. Workflow: parse the qmd → emit a sibling `.R` runner with one `tryCatch` per `{r}` chunk → run it → fix the source qmd → regenerate the runner → repeat until the PASS / FAIL / SKIP summary table is fully green; then commit the qmd fixes and do a final `quarto render`. Also use when a qmd whose YAML sets `execute: eval: false` has to be executed for real and must stop at the first error: `--mode execute` emits a fail-fast runner, launched through `resource-watched-run`.
In this repository17 other files it gives its agents.
- CLAUDE.mdCLAUDE.md
- agent-report-styleSkill
- creating-analysis-projectsSkill
- developing-r-packagesSkill
- git-hygieneSkill
- hugo-blogSkill
- md-formatSkill
- md-to-htmlSkill
- naming-conventionsSkill
- recommendation-letter-workflowSkill
- reporting-metadata-columnsSkill
- resource-watched-runSkill
- tailoring-applicationsSkill
- write-readmeSkill
- writing-labarchive-entriesSkill
- writing-qmd-scientificSkill
- writing-r-codeSkill
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18 rules. About 0 are common, 7 are distinctive, and 11 are very specific to this project.
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