Starter project · Intermediate
One analysis, two workflow engines
Calculate sequence GC content with a plain script, then reproduce the same output using Nextflow or Snakemake.
The question
How can explicit dependencies make a small analysis easier to run and verify?
Before you begin: Python and shell basics; install one workflow engine for the extension.
The data
Three tiny synthetic FASTA records shipped with the project. Ambiguous bases are counted separately and excluded from the GC denominator.
What you’ll make
- A per-sequence CSV summary
- A comparison against an exact expected result
- A dependency graph and a documented rerun experiment
Work through it
- Run the Python analysis and compare the CSV with expected.csv.
- Choose one engine and run its supplied workflow on the same input.
- Change one sequence, rerun, and inspect which task executes.
- Explain how a new quality-check step would connect to the existing workflow.
Read alongside the project
- Nextflow community training ↗
A guided route from running a first pipeline to composing and configuring workflows.
Course · Intermediate · Free · English - Snakemake general-use tutorial ↗
Build and extend an example workflow while learning dependency handling, configuration, and execution.
Tutorial · Intermediate · Free · English