A work-in-progress pipeline for crosslinking mass spectrometry analysis.
By default, it is assumed the end user will grant the docker container access to one or more raw files and the required xiSEARCH configuration files for linear and crosslinking searches. The paths to these inside the container can be specified in the pycross_config.toml file or on the command line when calling main.py. Any arguments specified on the command line override those present in the toml configuration file.
docker build -t pycross
docker run -it pycross bash
python /usr/pycross/main.py --toml /usr/pycross/pycross_config.toml- Add human friendly parsing for memory limit. E.G. Allowing 90GB or 90,000,000,000 instead of 90000000000.
- Update xiFDR version check to get the version string from calling xiSearch rather than hardcoding.
- Replace current input parsing with quantms ThermoRawFileParser module.
- Allow submodules to read from the command line if necessary for Nextflow integration.
- Replace xiSEARCH wrapper sections (linear search and crosslinking search) with direct calls to the .jar through Nextflow.
- Unit tests for:
- Input conversion
- Linear Search
- Mass Recalibration
- Crosslinking Search
- FDR Correction