Setup

Configuration

experiment_name

Refers to the common Xavier Lab naming convention of <date_initials>. This will help set the Google bucket location of the input and output files for the experiment; genomics_xavier_bucket/<experiment_type>/<experiment_name>. As is customary, the bcl files that serve as the input to the pipeline must be in genomics_xavier_bucket/<experiment_type>/<experiment_name>/bcl and the fastq files will be written to genomics_xavier_bucket/<experiment_type>/<experiment_name>/fastq.

experiment_type

Denotes the type of experiment that was run. It must correspond to one of the directories listed here, as this parameter is used to set the location for output.