Jorisvansteenbrugge · Aug 5, 2026 · Aug 5, 2026
diff --git a/.dockerignore b/.dockerignore
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
diff --git a/Dockerfile b/Dockerfile
diff --git a/README.md b/README.md
@@ -1,109 +1,46 @@
-# prs_utils
+# python_template
 
-![test](https://github.com/UMCUGenetics/prs_utils/actions/workflows/test.yml/badge.svg)
-![lint](https://github.com/UMCUGenetics/prs_utils/actions/workflows/lint.yml/badge.svg)
+![test](https://github.com/UMCUGenetics/python_template/actions/workflows/test.yml/badge.svg)
+![lint](https://github.com/UMCUGenetics/python_template/actions/workflows/lint.yml/badge.svg)
 
-Utility commands for the PRS pipeline, bundled as a single installable package.
+Python template project - This repository can be used as a starting point / guide on how to setup a python repository, including automated tests and code formatting.
 
-These utilities previously lived as standalone [PEP 723](https://peps.python.org/pep-0723/)
-scripts inside the `prsutils` Nextflow modules
-(`NF-Modules/modules/UMCUGenetics/prsutils/*/resources/usr/bin/`), each with its own
-`uv run --script` header and lock file. They are now one package with shared dependency
-resolution, linting and tests. The behaviour of every command is unchanged.
+## GitHub repository creation
 
-## Commands
+- Repository name: `Modules should have short, all-lowercase names. Underscores can be used in the module name if it improves readability. Python packages should also have short, all-lowercase names, although the use of underscores is discouraged.`
+- Add README
+- Add .gitignore: `python`
+- Add License: `MIT`
 
-Everything is reachable through the `prs-utils` entry point:
+Make sure to perform the following actions, after creating a new github repo:
 
-| Subcommand | Original script | NF module |
-| --- | --- | --- |
-| `prs-utils pgs-to-vcf` | `pgs_to_vcf.py` | `prsutils/getvcf` |
-| `prs-utils merge-prs-mqc` | `merge_prs_mqc.py` | `prsutils/mergeprsmqc` |
-| `prs-utils normalise-counts` | `normalise_counts.py` | `prsutils/norm` |
-| `prs-utils sample-qc` | `sample_qc.py` | `prsutils/sampleqc` |
-| `prs-utils get-snp-list` | `get_snp_list.py` | `prsutils/snplist` |
+- Create a develop branch.
+- Configure branch protection rules.
 
-Each subcommand keeps the argument parser it was written with, so the flags are identical to
-the standalone scripts. Use `prs-utils <subcommand> --help` for the per-command options.
+## UV
 
-```sh
-uv run prs-utils --help
-uv run prs-utils normalise-counts --PRS scores.tsv --mu 0.5 --SD 0.1 -o normalised.tsv
-uv run prs-utils get-snp-list --scoring_file PGS000004.txt --prefix PGS000004 --flank 100
-```
-
-Note that `merge-prs-mqc` takes its inputs as bare positional paths and always writes
-`prs_scores_mqc.tsv` in the working directory.
+UV supports packaged and unpackaged applications, this repository show cases a packaged application initiated with the command: `uv init --package .`. To create a simpler unpackaged application use: `uv init .`. Unpackaged applications can be used for single file scripts/tools, while packaged applications are used for (larger) tools requiring multiple files, distribution (pip) and tests separation.
 
-## Container image
-
-Each release publishes a multi-arch image to
-`ghcr.io/umcugenetics/prs-utils:<version>`, built from `uv.lock` so the dependency set is exactly
-the one the tests ran against. This is what the `prsutils` Nextflow modules pin their `container`
-directive to.
+Setup uv package and development dependencies:
 
 ```sh
-docker run --rm -v "$PWD:/data" -w /data ghcr.io/umcugenetics/prs-utils:1.0.0 \
-    prs-utils normalise-counts --PRS scores.tsv --mu 0.5 --SD 0.1 -o normalised.tsv
+uv init --package .
+uv add --dev ruff
+uv add --dev pytest
 ```
 
-Singularity pulls the same image directly:
+Run pytest and the python-template tool:
 
 ```sh
-singularity exec docker://ghcr.io/umcugenetics/prs-utils:1.0.0 prs-utils --version
-```
-
-Build it locally without publishing:
-
-```sh
-docker build -t prs-utils:dev .
-```
-
-## Releasing
-
-`prs-utils --version` prints the bare version from `pyproject.toml`, and the Nextflow modules
-capture that output into their `versions` topic and snapshot it. Keep the two repositories in step:
-
-1. Bump `version` in `pyproject.toml`.
-2. Run `uv lock` and commit the updated `uv.lock`.
-3. Tag and publish a GitHub release. The `publish.yml` workflow builds and pushes the image, then
-   fails the release if the image does not report the tagged version.
-4. Confirm the new tag appears under the repository's Packages.
-5. Bump the `container` tag in the five `prsutils` modules in
-   [UMCUGenetics/NF-Modules](https://github.com/UMCUGenetics/NF-Modules) and re-run their nf-tests.
-
-The first published version needs one manual step: set the GHCR package visibility to **public**
-(Package settings → Change visibility). Otherwise every `singularity pull` in CI and on the HPC
-needs registry credentials.
-
-## Development
-
-Setup and run the test suite:
-
-```sh
-uv sync
 uv run pytest tests
-```
-
-Linting and formatting use [Ruff](https://docs.astral.sh/ruff/):
-
-```sh
-uv run ruff check src tests
-uv run ruff format src tests
+uv run python-template World
+uv run python-template --help
 ```
 
 ## GitHub Actions
 
-This repository contains two GitHub actions workflows (`.github/workflows/`): `lint.yml` and
-`test.yml`. The lint workflow uses the [ruff-action](https://github.com/astral-sh/ruff-action)
-action to run ruff. The test workflow uses the
-[setup-uv action](https://github.com/astral-sh/setup-uv) to setup uv, install dependencies and
-run tests. Both actions are configured to run on each pull request and push to main and develop.
+This template project contains two GitHub actions workflows (`.github/workflos/`): `lint.yml` and `test.yml`. The lint workflow uses the [ruff-action](https://github.com/astral-sh/ruff-action) action to run ruff. The test workflow uses the [setup-uv action](https://github.com/astral-sh/setup-uv) to setup uv, install dependencies and run tests. Both actions are configured to run on each pull request and push to main and develop.
 
 ## pre-commit
 
-Git pre-commit hooks enable you to run certain commands before each commit and can be used to
-check code style before committing. The file `.pre-commit-config.yaml` contains the
-[Ruff](https://docs.astral.sh/ruff/) [pre-commit](https://pre-commit.com) hook, which will
-automatically run Ruff before each commit. Run the following command to install the git commit
-hook: `uvx pre-commit install`.
+Git pre-commit hooks enable you to run certain commands before each commit and can be used to check code style before committing. The file `.pre-commit-config.yaml` contains the [Ruff](https://docs.astral.sh/ruff/) [pre-commit](https://pre-commit.com) hook, which will automatically run Ruff before each commit. Run the following command to install the git commit hook: `uvx pre-commit install`.
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,14 +1,13 @@
 [project]
-name = "prs-utils"
-version = "1.0.0"
-description = "Utility commands used by the UMCUGenetics prsutils Nextflow modules."
+name = "python-template"
+version = "0.1.0"
+description = "Python template project."
 readme = "README.md"
 authors = [
     { name = "Bioinformatica Genetica", email = "bioinformatica-genetica@umcutrecht.nl" }
 ]
-requires-python = ">=3.12"
+requires-python = "~=3.14.0"
 dependencies = [
-    "pandas>=2.2",
     "typer>=0.26.8",
 ]
 
@@ -20,7 +19,7 @@ dev = [
 ]
 
 [project.scripts]
-prs-utils = "prs_utils.cli:cli"
+python-template = "python_template.cli:cli"
 
 [build-system]
 requires = ["uv_build>=0.11.27,<0.12"]

diff --git a/src/prs_utils/cli.py b/src/prs_utils/cli.py