This repository is a pipeline for processing raw or mzML files through msconvert, msfragger, and percolator.
The workflow has the following logic
- If raw files are provided as input, will process these files using msconvert converting them to mzML files
- The mzML files are processed with MSFragger utilizing an input parameter file and fasta database
- The pin output files are processed with Percolator and target/decoy PSM files are combined
- The result is a pepXML file per input file and a pout file (Percolator output file) per input file as well
Some caveats
- If raw files are provided the files are converted to mzML with msconvert
- If mzML files are provided this step is skipped and mzML files are immediately processed with MSFragger
- Input can be a comma separated string of files I.e. "file1.raw,file2.raw,file3.raw"
- Or input can be a directory containing .raw or .mzML files like "/path/to/files/*.raw"