Repeatable processing.
WHAT A PIPELINE IS
A defined sequence of tools processing data from raw input to result.
WHY THEY ARE FORMALISED
Analyses involve many steps, each with parameters, and reproducing them by hand is unreliable.
WHAT WORKFLOW SYSTEMS PROVIDE
Declaring steps and their dependencies Parallel execution where steps are independent Resuming after failure Portability across computing environments A record of what ran
WHAT CONTAINERS ADD
Exact tool versions, so the environment is reproducible.
WHY THAT MATTERS ENORMOUSLY
Tool versions change results, and undocumented versions make an analysis irreproducible.
WHAT TO PIN
Every tool version, every reference, every parameter.
WHAT TO STORE WITH RESULTS
The exact configuration that produced them.
WHAT TO AUTOMATE
The whole path from raw data to figures.
WHY
So a corrected input regenerates everything, correctly.
WHAT TO AVOID
Manual steps Undocumented filtering Spreadsheets in the middle of a pipeline
WHY THAT LAST POINT
Spreadsheet software alters values on import, silently, and has corrupted published datasets.
WHAT TO TEST
That someone else can run the pipeline and obtain the same result.
