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pipelines
// Source of truth for choosing and combining computational-execution skills (Snakemake, marimo, RunPod). Load when planning the orchestration shape of an analysis after methodology is decided.
// Source of truth for choosing and combining computational-execution skills (Snakemake, marimo, RunPod). Load when planning the orchestration shape of an analysis after methodology is decided.
[HINT] Download the complete skill directory including SKILL.md and all related files
| name | pipelines |
| description | Source of truth for choosing and combining computational-execution skills (Snakemake, marimo, RunPod). Load when planning the orchestration shape of an analysis after methodology is decided. |
Decision aid for execution shape. Load only after methodology is decided
(see skills/INDEX.md and science-plan-analysis). Picking an execution
substrate before the analysis question is specified usually produces ceremony
without rigor.
For analysis-readiness planning, start at ../INDEX.md or run
science-plan-analysis.
| Skill | Load when | Avoid when |
|---|---|---|
snakemake.md | Multi-step pipeline with file dependencies; intermediates worth caching; reproducible re-runs matter | One-off exploration; no DAG of dependencies |
marimo.md | Interactive exploration; parameter sweeps; presentation with widgets; pre-pipeline prototyping | Production batch; long jobs; CI |
runpod.md | Short-lived rented GPU; uv-based project; workload too large/slow for workstation | Long-lived managed cluster; CPU-only work |
These three are not mutually exclusive: marimo for prototyping -> snakemake
for the pipeline -> runpod for the GPU rule. The hub records the decision
order; the leaves cover the mechanics.
science-plan-pipeline produces tool-agnostic
task lists. Only commit to a specific orchestration substrate after the task
list stabilizes.protected() does not save you from cleanup-before-rerun (see
snakemake.md "protected() does NOT prevent rerun-cleanup"). Apply the
marker-file pattern to any rule whose outputs live outside out_dir.datapackage.json). Without all three the
pipeline is decorative.../data/SKILL.md — input-data conventions; pipelines should read from data/raw/ and write to data/processed/ or results/.../research/research-package-spec.md — terminal rule should produce a research package.../statistics/SKILL.md — statistical decisions that should be made before pipeline construction.