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Organize multi-step scientific analyses into reproducible, self-contained modules.
Passed 17 of 21 test cases with the skill, and 16 of 21 without it.
and 1 more in the full report
3 fixed15 passed either way2 still failing2 broke
Tokens, turns and time describe resource use, not a dollar price.
One of 3 test cases the skill fixed. Same model, same prompt, with and without the skill.
I'm beginning a new RNA-seq project that involves quality control, differential expression, and gene set enrichment analysis. I need help organizing this multi-step pipeline into clean analysis stages. Please help me establish the directory layout for each stage, set up the script and output locations, and draft the required documentation files to track our computational methods, exact software versions, and script commands.
| Checked | Without skill | With skill |
|---|---|---|
| Each stage directory uses subdirectories for scripts, output/figures, and output/tables. | Missed | Passed |
| Software versions in stage documentation files are recorded using specific package version lookup APIs rather than full environment exports. | Missed | Passed |
The instructions your model reads when the skill loads.
Use this skill for a scientific workflow with two or more analysis stages or
when a stage produces scripts plus result files. It defines project
organization and methods capture; load figure-style as well whenever a stage
creates or revises a plot.
Before writing outputs, list the modules and the dependency edges between them.
Use stable ASCII names. Conventional acronyms such as QC, PCA, DEG, and
GSEA may stay uppercase; otherwise prefer a short kebab-case name.
Respect a compatible layout that already exists. Do not reorganize unrelated user files merely to impose this convention.
Create only directories the module actually needs:
<module>/
├── scripts/
├── input/
├── output/
│ ├── figures/
│ └── tables/
└── README.md
scripts/ contains the executable source for this module.input/ contains small module-specific inputs or a manifest/reference to the
canonical data. Do not duplicate a large dataset by default.output/figures/ contains rendered figures from this module only.output/tables/ contains machine-readable results from this module only.README.md is the module's reproducibility record and methods source.Shared immutable/raw data may live in project-level data/. A downstream module
references an upstream output by a project-relative path; it does not silently
copy or rename that output.
test cases passed, vs 16 / 21 without
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