Advanced configuration

The pipeline options are described in the CLI help. Run baysor --help or the corresponding command like baysor run --help for the list of main options.

However, there are additional parameters that can be specified through the TOML config. See example_config.toml for their description. All parameters from the config can also be passed through the command line. For example, to set exclude_genes from the data section you need to pass --config.data.exclude-genes='Blank*,MALAT1' parameter. Please, keep in mind that the CLI parameters require replacing all underscores (_) with -.

For more details on the syntax for CLI arguments, see the Comonicon documentation. TL;DR, possible spelling options are: --x-column X or -x X, also --x-column=X or -xX. And if you're using strings with unusual symbols like * or ?, it's better to have them in quotes: --config.data.exclude-genes='Blank*'.

Multi-threading

All running options support some basic multi-threading. To enable it, set JULIA_NUM_THREADS environment variable before running the script You can either do it globally by running export JULIA_NUM_THREADS=13 or for an individual command:

JULIA_NUM_THREADS=13 baysor run -m 30 -s 30 ./molecules.csv

The latest julia version is recommended, as multi-threading is being actively developed in julia.