Reproducible Pipelines

Reference for building reproducible research pipelines: from project directory structure to automated workflows to journal-ready replication packages. Every computational result should be regenerable from raw data by running a single command.

When to Use This Skill

Use when the user is:

• Setting up a new empirical research project
• Building or debugging a Makefile/Snakemake/DVC pipeline
• Preparing a replication package for journal submission
• Managing computational environments (conda, Docker, renv)
• Tracking data provenance or versioning large datasets
• Debugging "works on my machine" reproducibility failures

Skip when:

• The task is about estimation methodology (use causal-inference or structural-modeling skill)
• The task is git workflow management (see workflows-work/references/worktree-patterns.md)
• The task is about orchestrating Claude agents (see slfg/references/orchestration-patterns.md)

Where to Start

• New project? Start with Directory Structure below
• Adding a workflow manager? Jump to Workflow Managers (Make / Snakemake / DVC)
• Preparing for submission? Jump to Pre-Submission Checklist

Project Directory Structure

Use a standardized layout from the start. This is the structure expected by most replication reviewers:

project/
├── README.md                 # Master documentation (how to replicate)
├── Makefile                  # Or Snakefile — single entry point
├── environment.yml           # Conda environment (or requirements.txt)
├── data/
│   ├── raw/                  # Original, immutable data files
│   │   └── README.md         # Data sources, access instructions, citations
│   ├── intermediate/         # Cleaned/transformed data (gitignored, regenerable)
│   └── final/                # Analysis-ready datasets (gitignored, regenerable)
├── code/
│   ├── 01_clean.py           # Data cleaning
│   ├── 02_build.py           # Variable construction, merges
│   ├── 03_estimate.py        # Main estimation
│   ├── 04_robustness.py      # Robustness checks
│   └── 05_tables_figures.py  # Output generation
├── output/
│   ├── tables/               # LaTeX/CSV tables (gitignored, regenerable)
│   └── figures/              # PDF/PNG figures (gitignored, regenerable)
├── docs/
│   ├── brainstorms/          # Research brainstorming docs
│   ├── plans/                # Implementation plans
│   └── codebook.md           # Variable definitions
├── tests/                    # Validation tests
│   ├── test_clean.py
│   └── test_estimates.py
└── paper/
    └── manuscript.tex        # The paper itself

Key principles:

• data/raw/ is immutable — never modify raw data files
• Everything in intermediate/, final/, output/ is regenerable — gitignore it
• Number scripts to indicate execution order (or rely on the workflow manager)
• Keep README.md as the single entry point for replicators

.gitignore for Research Projects

# Data (too large for git; document in README how to obtain)
data/raw/*.csv
data/raw/*.dta
data/raw/*.parquet
data/intermediate/
data/final/

# Generated output (reproducible from code)
output/tables/
output/figures/

# Environment
.conda/
__pycache__/
*.pyc
.ipynb_checkpoints/

# Large files managed by DVC
*.dvc

# OS
.DS_Store
Thumbs.db

# IDE
.vscode/
.idea/

Workflow Managers

Make (Recommended Default)

Make is universally available, well-understood, and sufficient for most research pipelines. Use it unless you have a specific reason for something else.

# Makefile — Top-level research pipeline

.PHONY: all clean tables figures

# Default target: reproduce everything
all: output/tables/main_results.tex output/figures/event_study.pdf

# === DATA CLEANING ===
data/intermediate/clean.parquet: data/raw/survey_2020.csv code/01_clean.py
	python code/01_clean.py

# === VARIABLE CONSTRUCTION ===
data/final/analysis.parquet: data/intermediate/clean.parquet code/02_build.py
	python code/02_build.py

# === ESTIMATION ===
output/estimates/main.pkl: data/final/analysis.parquet code/03_estimate.py
	python code/03_estimate.py

output/estimates/robustness.pkl: data/final/analysis.parquet code/04_robustness.py
	python code/04_robustness.py

# === TABLES AND FIGURES ===
output/tables/main_results.tex: output/estimates/main.pkl output/estimates/robustness.pkl code/05_tables_figures.py
	python code/05_tables_figures.py --tables

output/figures/event_study.pdf: output/estimates/main.pkl code/05_tables_figures.py
	python code/05_tables_figures.py --figures

# === UTILITIES ===
clean:
	rm -rf data/intermediate/ data/final/ output/

tables: output/tables/main_results.tex
figures: output/figures/event_study.pdf

Make best practices:

• Each target lists its exact dependencies (both data and code)
• Changing any dependency triggers recomputation of downstream targets
• make -j4 runs independent targets in parallel (e.g., tables and figures simultaneously)
• make -n dry run shows what would be executed without running anything
• Use .PHONY for targets that don't correspond to files

Snakemake (For Complex Pipelines)

Use Snakemake when the pipeline has many steps, parameter sweeps, or needs cluster execution.

# Snakefile

configfile: "config.yaml"

rule all:
    input:
        "output/tables/main_results.tex",
        "output/figures/event_study.pdf"

rule clean_data:
    input:
        raw="data/raw/survey_2020.csv"
    output:
        clean="data/intermediate/clean.parquet"
    script:
        "code/01_clean.py"

rule build_analysis:
    input:
        clean="data/intermediate/clean.parquet"
    output:
        analysis="data/final/analysis.parquet"
    script:
        "code/02_build.py"

rule estimate:
    input:
        data="data/final/analysis.parquet"
    output:
        estimates="output/estimates/{spec}.pkl"
    params:
        seed=config["seed"]
    script:
        "code/03_estimate.py"

# Snakemake advantages over Make:
# - Python syntax (easier for researchers)
# - Built-in wildcards for parameter sweeps
# - Cluster execution (SLURM, SGE)
# - Conda environment per rule
# - Automatic DAG visualization: snakemake --dag | dot -Tpdf > dag.pdf

DVC (Data Version Control)

Use DVC when you need to version large data files that don't fit in git.

# Initialize DVC in an existing git repo
dvc init

# Track a large data file
dvc add data/raw/survey_2020.csv
# Creates data/raw/survey_2020.csv.dvc (small metadata file, tracked by git)
# The actual data is in .dvc/cache

# Configure remote storage
dvc remote add -d myremote s3://my-bucket/dvc-cache

# Push data to remote
dvc push

# Collaborator pulls data
dvc pull

DVC pipeline integration:

# dvc.yaml
stages:
  clean:
    cmd: python code/01_clean.py
    deps:
      - data/raw/survey_2020.csv
      - code/01_clean.py
    outs:
      - data/intermediate/clean.parquet

  estimate:
    cmd: python code/03_estimate.py
    deps:
      - data/final/analysis.parquet
      - code/03_estimate.py
    outs:
      - output/estimates/main.pkl
    params:
      - seed
      - n_bootstrap

Enhanced DVC: remote storage and experiment tracking:

# Remote storage options
dvc remote add -d s3remote s3://my-bucket/dvc-cache      # AWS S3
dvc remote add -d gcsremote gs://my-bucket/dvc-cache     # Google Cloud
dvc remote add -d sshremote ssh://server.edu/path/cache  # SSH server (common for university HPC)
dvc remote add -d localremote /data/shared/dvc-cache     # Shared NFS mount

# Visualize pipeline DAG
dvc dag                        # ASCII DAG in terminal
dvc dag --dot | dot -Tpdf > pipeline.pdf  # PDF visualization

# Parameter tracking and comparison
# params.yaml — centralize all tunable parameters
# DVC auto-tracks params files listed in dvc.yaml

dvc params diff HEAD~1         # Compare current params to last commit
dvc params diff main feature-branch  # Compare across branches

# Metrics: track experiment outcomes
# In dvc.yaml: add metrics: [output/metrics.json] to a stage
dvc metrics show               # Show all tracked metrics
dvc metrics diff HEAD~3        # Compare metrics across commits

# Partial pipeline execution
dvc repro estimate             # Run only the 'estimate' stage and its deps
dvc repro --force              # Re-run even if inputs haven't changed

# Pull only what you need (for large datasets)
dvc pull data/final/analysis.parquet.dvc  # Pull only one file
dvc fetch --run-cache          # Prefetch cached stage outputs

DVC best practices for research:

• Commit dvc.lock to git — it records the exact state of all outputs
• Use params.yaml for all tunable parameters (seeds, model specs, sample cutoffs); DVC tracks changes automatically
• On HPC clusters: configure SSH remote pointing at shared storage so collaborators don't re-run expensive stages
• dvc metrics is useful for tracking bias/RMSE across Monte Carlo runs; commit metrics.json to see history

Which Workflow Manager to Use

Factor	Make	Snakemake	DVC	pytask
Complexity	Simple pipelines (< 20 targets)	Complex pipelines, parameter sweeps	Data-heavy pipelines	Mixed-language projects
Learning curve	Low (most researchers know it)	Medium (Python-like syntax)	Medium (git-like commands)	Medium (Python decorators)
Cluster support	Manual (submit scripts)	Built-in (SLURM, SGE)	Via CML	Via plugins
Data versioning	No	No	Yes (core feature)	No
Availability	Everywhere	pip install	pip install	pip install
Reviewer familiarity	Very high	Medium	Lower	Lower

pytask (Python-Native DAG)

pytask — Python-native DAG manager using decorated functions with type-annotated dependencies. First-class plugins for Stata, R, Julia. pixi run pytask rebuilds the entire project. Good for mixed-language economics projects.

Recommendation: Start with Make. Switch to Snakemake if you need cluster execution or parameter sweeps. Add DVC if data files are too large for git. Consider pytask if your team prefers Python-native tooling and works across multiple languages.

Additional References

• references/stata-and-crosslang.md — Stata master.do patterns, batch mode, ado versioning, Stata anti-patterns; cross-language tolerance thresholds (R/Stata/Python) and systematic discrepancy trap table
• references/environment-and-seeds.md — conda/renv/Docker environment management, random seed management by language, results caching strategies
• references/replication-package.md — AEA-compliant replication package structure: README template, data availability statement, computational requirements, output map

Common Anti-Patterns

Anti-Pattern	Problem	Better Approach
Jupyter notebooks as the pipeline	Non-linear execution, hidden state, hard to automate	Use .py scripts orchestrated by Make; notebooks only for exploration
Absolute file paths (/Users/me/data/...)	Breaks on any other machine	Use relative paths from project root; configure data directory in a single config file
pip install without version pinning	Package updates break code silently months later	Pin exact versions: pandas==2.2.0
Modifying raw data files	Destroys provenance; can't rerun from original	data/raw/ is immutable; all cleaning produces new files in data/intermediate/
Committing large data files to git	Bloats repository, slow clones	Use DVC, git-lfs, or document download instructions
Hardcoded random seeds scattered across files	Hard to find, easy to miss one	Centralize in config.py, derive all seeds from one master seed
"It works on my laptop"	Different OS, library versions, locale settings	Test in Docker or CI; provide environment.yml
Results tables copy-pasted into paper	Tables get stale when estimates change	Generate LaTeX tables directly from estimation code
Pipeline only tested by the author	Missing implicit dependencies	Have a co-author or RA run from scratch; or use CI

The reproducibility-auditor agent can audit pipelines for these anti-patterns and verify replication packages before submission.