https://github.com/daisybio/domainsplit
A nextflow pipeline to split domain-domain interaction data into train, validation, and test while reducing data leakage and bias.
https://github.com/daisybio/domainsplit
Last synced: about 1 month ago
JSON representation
A nextflow pipeline to split domain-domain interaction data into train, validation, and test while reducing data leakage and bias.
- Host: GitHub
- URL: https://github.com/daisybio/domainsplit
- Owner: daisybio
- License: mit
- Created: 2026-05-15T14:02:09.000Z (2 months ago)
- Default Branch: main
- Last Pushed: 2026-06-09T20:52:34.000Z (about 2 months ago)
- Last Synced: 2026-06-09T22:14:24.927Z (about 2 months ago)
- Language: Nextflow
- Size: 274 KB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: docs/CONTRIBUTING.md
- License: LICENSE
- Citation: CITATIONS.md
Awesome Lists containing this project
README
# daisybio/domainsplit
[](https://github.com/codespaces/new/daisybio/domainsplit)
[](https://github.com/daisybio/domainsplit/actions/workflows/nf-test.yml)
[](https://github.com/daisybio/domainsplit/actions/workflows/linting.yml)[](https://doi.org/10.5281/zenodo.XXXXXXX)
[](https://www.nf-test.com)
[](https://www.nextflow.io/)
[](https://github.com/nf-core/tools/releases/tag/4.0.2)
[](https://docs.conda.io/en/latest/)
[](https://www.docker.com/)
[](https://sylabs.io/docs/)
[](https://cloud.seqera.io/launch?pipeline=https://github.com/daisybio/domainsplit)
## Introduction
**daisybio/domainsplit** is a bioinformatics pipeline that ...
This directory contains a Nextflow pipeline that downloads and processes all required public databases (3did, UniProt, Negatome, STRING, Pfam, pfam2go) to generate the `domainsplit.sqlite3` database of domain-domain interactions, then splits it into train/validation/test partitions using several leakage-reduction strategies.
## Usage
> [!NOTE]
> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.
Now, you can run the pipeline using:
```bash
nextflow run daisybio/domainsplit \
-profile \
--outdir
```
> [!WARNING]
> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/running/run-pipelines#using-parameter-files).
## Output
The main output is the SQLite database file `domainsplit.sqlite3` in the `results` directory, plus per-method, per-split databases under `results/split_databases//.sqlite3`.
## Notes
- Each process in `main.nf` is commented for clarity.
- Some processes require external scripts (e.g., `mysql2sqlite` for 3did conversion).
- You may need to adjust paths or URLs as needed.
## Environment variables
Some processes require secrets passed via environment variables. Copy `.env.example` to `.env` and fill in your values — the `.env` file is gitignored.
| Variable | Required | Description |
| ---------- | -------------------- | --------------------------------------------------------------------------------------------------------------- |
| `HF_TOKEN` | Yes (ESM embeddings) | HuggingFace access token for downloading ESM model weights. Obtain at . |
On a SLURM cluster, export the variable in your job script or pass it as a [Nextflow secret](https://www.nextflow.io/docs/latest/secrets.html):
```bash
nextflow secrets set HF_TOKEN
```
## Credits
daisybio/domainsplit was originally written by Konstantin Pelz, Christian Romberg, Chiara Thomas.
We thank the following people for their extensive assistance in the development of this pipeline:
## Contributions and Support
If you would like to contribute to this pipeline, please see the [contributing guidelines](docs/CONTRIBUTING.md).
## Citations
An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).
> **The nf-core framework for community-curated bioinformatics pipelines.**
>
> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
>
> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).