lehtiolab/nf-deqms

A small pipeline to re-run DEqMS on existing results

Introduction

This workflow reruns DEqMS analysis on existing results, e.g. from the lehtiolab/ddamsproteomics pipeline. It exists so one can use orthogonal sample groups (CTRL vs TREAT, old vs young) and rerun, or perhaps correct a mistake in the sample annotation, without having to re-search an entire set of spectra against a protein sequence database.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.

How to run

• install Nextflow
• install Docker, Singularity, or Conda
• run pipeline:

nextflow run lehtiolab/nf-deqms --proteins proteins.txt --peptides peptides.txt --genes genes.txt --ensg ensg.txt --sampletable samples.txt -profile standard,docker

You can leave out any accession that you do not have or are not interested in (e.g. --ensg in a Swissprot analysis).

The lehtiolab/nf-deqms pipeline comes with documentation about the pipeline, found in the docs/ directory:

• Running the pipeline
• Output and how to interpret the results
• Troubleshooting

There is more extensive documentation on the options inside the main.nf file.

Credits

lehtiolab/nf-deqms was originally written by Jorrit Boekel and tries to follow the nf-core best practices and templates.