![lehtiolab/nf-msconvert]

Runs msconvert in docker to convert RAW to mzML.

Introduction

This is a small Nextflow pipeline that just wraps and runs the Proteowizard docker container to leverage msconvert from that software package.

Quick Start

i. Install nextflow

ii. Install one of docker, singularity

iii. Download the pipeline and run on your raw files to convert. Example:

# Semicolons to separate raws, options, filters, remove the `--` from the options as they are otherwise passed to nextflow, and use double quoting for options/filters.
nextflow run lehtiolab/nf-msconvert -profile <docker/singularity> --raws '/path/to/*.raw' --options 'mz5;numpressAll' --filters '"peakPicking true 2";"precursorRefine"'
nextflow run lehtiolab/nf-msconvert -profile <docker/singularity> --raws '/path/to/1.raw;/path/to/2.raw' --options 'mz5;numpressAll' --filters '"peakPicking true 2";"precursorRefine"'

See usage docs for all of the available options when running the pipeline.

Documentation

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

1. Installation
2. Pipeline configuration
   • Local installation
3. Running the pipeline
4. Troubleshooting