LTEE project

What you hand in for the project you build in the lessons

How the LTEE project is assessed: your own ltee-project repository on GitHub, built step by step in the hands-on parts of the lessons, released and archived on Zenodo with a DOI.

Note

How the 40% is split between the items below is to be confirmed.

What it is

The LTEE project is the project you build in the hands-on parts of the lessons, from lesson 02 to lesson 12: the same analysis and the same data for everyone (about the project). It counts for 40% of the course grade.

It is assessed separately from the capstone (30%), in which you apply the same skills to your own research project.

What you hand in

When you have finished lesson 12:

The address of your ltee-project repository on GitHub. It must be public, because Zenodo archives only public repositories.
The DOI of its released version from Zenodo (lesson 12, section 3). The DOI badge is at the top of your README, and the DOI is in CITATION.cff.

What your repository shows

Each lesson adds something. All of it should be in the released version:

Lesson	In your repository
02	the layout from the course template
03	`scripts/download_data.py`; `metadata/sources.tsv`, `checksums.sha256` and `samples.tsv`; no raw data in Git
04	a history of small, described commits; the tag `lesson-04`; a merged pull request, and from then on one pull request per lesson
05	`pixi.toml` and `pixi.lock`, committed together; the tasks, ending in `reproduce`; a green Reproduce check on GitHub
06, 07	`notebooks/explore-reads.ipynb` with outputs cleared; `reports/ltee-report.qmd`, rendered by `pixi run reproduce`
08	`containers/Dockerfile`, which builds the environment from `pixi.lock`
09	`workflow/Snakefile`, run by `reproduce`; `pixi run compare-to-shell` reports identical variants; the variants section of the report
10	`workflow/nextflow/main.nf`; `pixi run compare-workflows` reports identical variants
11	a README that answers the seven questions; `LICENSE`; a valid `CITATION.cff`; `CONTRIBUTING.md` and `CODE_OF_CONDUCT.md`; `docs/software-versions.txt`
12	a release (`v1.0.0`) on GitHub, archived on Zenodo with a DOI

The report gives the expected variant counts (the LTEE project).

The history matters as well as the final files: the commits, tags and pull requests from the lessons show how the project was built.

How it is checked

The Reproduce GitHub Action on the released version: a fresh machine, a clean clone, pixi install --locked, pixi run reproduce. Green or red.
The automatic checks, listed by the same script as for the capstone (pixi run check-capstone PATH in the course repository). The finished project in the course repository passes all of them once it has a DOI.
A reading of the repository and its history, against the table above.

You can run 1 and 2 yourself at any time.

Self-check before you hand in

# In a new folder, as a grader would:
git clone git@github.com:YOU/ltee-project.git check && cd check
pixi install --locked
pixi run reproduce
pixi run compare-workflows
pixi exec cffconvert --validate -i CITATION.cff
git tag            # v1.0.0 is there

And from the course repository: pixi run check-capstone ../check.