Internal QC and mzML precursor refining pipeline

A nextflow pipeline to run QC for proteomics instruments. Handles Thermo and Bruker DDA and DIA runs, the output is a qc.json file with some statistics, such as nr of scans, peptides, precursor error (quartiles), retention times, etc.

Usage

Mainly internal to our lab, but an example is:

nextflow run -resume -profile docker qc.nf \
    --dia \
    --db your-peptides.fa \
    --library your-peptides.speclib \
    --instrument [timstof, qe] \ # pick one of these
    --raw your-QC-run.raw 

Use --dda instead of --dia and remove the --library param when running DDA data. When testing on github, instead of --raw, we use --mzml to keep files small.

Development

Install Nextflow and Docker. For local work, test with:

# This also runs on github actions
bash run_tests.sh

# Locally, supply your own raw files which are too big for GHA
bash run_tests_local.sh

On github actions we run on PR/push to master.

Releasing

Create a PR, make changes, update the version etc. Make sure you publish a release to update the container (or push that by hand).

Todo:

• Block PRs where there is no version change