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

Development

Running Tests

We use the pytest Python package to run our tests. It can be installed using conda:

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:

docker pull ghcr.io/talusbio/nf-encyclopedia:latest
pytest

References

This pipeline uses code and infrastructure developed and maintained by the nf-core initiative, and reused here under the MIT 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.