A small pipeline to re-run DEqMS on existing results
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.
- 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:
There is more extensive documentation on the options inside the main.nf file.
lehtiolab/nf-deqms was originally written by Jorrit Boekel and tries to follow the nf-core best practices and templates.