Internal QC and mzML precursor refining pipeline

Usage

Mainly internal, but if you must:

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

When testing, instead of --raw, we use --mzml to keep files small.

Development

For local work:

bash run_tests.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.

Todo:

• Block PRs where there is no version change
• Fix local testing script