lehtiolab/nf-msconvert

Runs conversion of .raw/.d files to .mzML format

Introduction

This is a small lehtiolab-internal Nextflow pipeline that just wraps and runs the Proteowizard or ThermoRawFileParser container to convert files in a nextflow pipeline

Quick Start

i. Install nextflow

ii. Install one of docker, singularity, 'apptainer'

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.
# --reportout gives a small amount of pipeline run reports (process trace, CPU usage, etc).
nextflow run lehtiolab/nf-msconvert -profile docker -resume \
  --raws '/path/to/*.raw' \
  --options 'mz5;numpressAll' \
  --filters "precursorRefine"' \
  --centroid '1,2' \
  --reportout

# Default uses proteowizard, if that does not work or another tool is preferred, you can use `--mzmltool thermorawfileparser`. Here we also pass --md5out to get MD5 sums of each mzML file.
# NB it does not take --options and --filters
nextflow run lehtiolab/nf-msconvert -profile singularity -resume \
  --raws '/path/to/1.raw;/path/to/2.raw' \
  --centroid 2 \
  --md5out \
  --mzmltool thermorawfileparser