https://github.com/talusbio/nf-encyclopedia
A NextFlow pipeline for chromatogram library DIA proteomics workflows
https://github.com/talusbio/nf-encyclopedia
bioinformatics data-independent-acquisition nextflow pipeline proteomics workflow
Last synced: 6 months ago
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A NextFlow pipeline for chromatogram library DIA proteomics workflows
- Host: GitHub
- URL: https://github.com/talusbio/nf-encyclopedia
- Owner: TalusBio
- License: apache-2.0
- Created: 2021-10-15T17:50:02.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2023-12-04T23:16:24.000Z (over 2 years ago)
- Last Synced: 2025-12-09T09:02:18.375Z (7 months ago)
- Topics: bioinformatics, data-independent-acquisition, nextflow, pipeline, proteomics, workflow
- Language: Nextflow
- Homepage:
- Size: 18.4 MB
- Stars: 7
- Watchers: 1
- Forks: 4
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
- Citation: CITATION.md
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README
# nf-encyclopedia
nf-encyclopedia is a NextFlow pipeline specifically designed to analyze DIA proteomics experiment that leverage chromatogram libraries; however it is perfectly suited to analyze DIA proteomics experiments without chromatogram libraries as well.
The nf-encyclopedia connects three open-source tools---MSconvert, EncyclopeDIA, and MSstats---to go from mass spectra to quantified peptides and proteins.
See the [nf-encyclopedia documentation](https://TalusBio.github.io/nf-encyclopedia)
## Development
### Running Tests
We use the [pytest](https://docs.pytest.org/en/7.0.x/contents.html) Python package to run our tests. It can be installed using conda:
``` sh
conda env create --name nf_encyclopedia --file=environment.yml
conda activate nf_encyclopedia
conda install pytest
```
Once installed, tests can be run from the root directory of the workflow.
Run them with:
``` sh
docker pull ghcr.io/talusbio/nf-encyclopedia:latest
pytest
```
## References
This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) initiative, and reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/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.
## Credits
This pipeline was originally written by @ricomnl and @wfondrie at Talus Bio.
Additionally, @cia23 has spent numerous hours reviewing @wfondrie's messy PRs and performing validation experiments.