"description":"Turn on saving of KrakenUniq per-read taxonomic assignment file",
"help_text":"Save a text file that contains a list of each read that had a taxonomic assignment, with information on specific taxonomic taxonomic assignment that that read recieved.\n\n> Modifies tool parameter(s):\n> - krakenuniq: `--output`"
},
"krakenuniq_batch_size":{
"type":"integer",
"default":20,
"fa_icon":"far fa-window-restore",
"description":"Set the batch size for KrakenUniq",
"help_text":"Specify the batch size for KrakenUniq. The reference database for KrakenUniq is loaded into memory once in a process and then used to classify many samples. This parameter determines for how many samples at a time."
},
"run_bracken":{
"type":"boolean",
"description":"Turn on Bracken (and the required Kraken2 prerequisite step).",