Configuration

We use a config file to pass variables to the IMP engine.

The default parameters are visible in <src>/src/config.imp.json. You could override some parameters via the user configuration file userconfig.imp.json that you can give on the runtime.

With impy:

impy -c /path/to/config.json <command>

With snakemake:

CONFIGFILE="/path/to/config.json" snakemake

Note that if you are entered the docker container with impy -c /path/to/config.json --enter <command> , this parameter is already set.

Configuration file must be a valid JSON file:

e.g.:

{
    "threads": 8,
    "output": /home/user/analysis_output_directory,
    "preprocessing_filtering": false
}

Available parameters

Per tool/step parameters

Trimmomatic

Following parameters are taken from the Trimmomatic documentation:

idba_ud

vizbin

filtering

sortmerna

prokka

kegg



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