config.md

Configuration files

🧸 Notes, no API decisions

1. Program configuration file
2. Experiment configuration file (protocol)

Program configuration

• Path to reference database default directory
• Path to default log directory

[refs]
default_dir=/path/to/dir
last_download_dir=/lastpath/used/by/getdb
default_db={name_of_default_db: in default_dir}
default_db_its={... : used when --its is activated}

[defaults]
threads={int}
strategy=
notification={0,1}
crosstalk={0,1}
multiqc={0,1}

Experiment

• All parameters?