File Modification Rules (CRITICAL)

General Rules (All Projects)

Never Overwrite These Files

1. Outputs from someone else — files from collaborators, students, or external sources
2. Original/source data — anything you did not generate in this session
3. Configuration files — unless the user explicitly requests changes

Instead

• Create a new file with an updated name (e.g., add _updated, _with_new_column)
• Ask the user before modifying if uncertain about the file's origin

Files You CAN Overwrite

• Files you created in the current session
• Configuration files when the user requests changes

Script Output Integrity

Never create standalone scripts solely to modify outputs from other scripts.

If modifications are needed:

1. Modify the original script — if the change belongs upstream, update the source (ask user first)
2. Handle in downstream scripts — do the transformation as part of the consuming script's workflow

Do NOT create intermediate "fixer" scripts that modify upstream outputs after the fact — this breaks the reproducibility chain between scripts and their outputs.

When Uncertain

If you're not sure whether a file is safe to overwrite, ask:

• "This file exists — was it generated by another script or provided externally?"
• "Should I create a new file with a modified name, or is it safe to overwrite?"

Data Science Projects (with data/ and outs/ directories)

These additional rules apply in projects with project-type: data-science or that use the script-organization conventions (numbered scripts, data/ for inputs, outs/ for outputs).

Output Ownership

Each script writes only to its own output folder under outs/. Never write to another script's output folder.

# Script 03_plots.qmd writes ONLY to:
out_dir <- here("outs/03_plots")

# NEVER write to another script's folder:
# here("outs/01_analysis/modified_data.rds")  # WRONG

data/ is Read-Only

Scripts never write to data/. This directory contains only external/immutable inputs (raw data, collaborator files, annotations). If your code produced it, it goes in outs/.

Example

# BAD: Creating a script to add Gene.short to another script's output
# This disconnects the file from the script that produced it

# GOOD: Downstream plotting script joins against lookup at runtime
limma_res <- readRDS(here("outs/01_analysis/limma_results_annotated.rds")) %>%
  left_join(gene_name_lookup, by = "trinity_gene_id")