Run KRAKEN2 for each cell
Usage
BascetRunKraken(
bascetRoot,
useKrakenDB = "/data/henlab/kraken/standard-8",
numLocalThreads = NULL,
inputName = "asfq",
outputName = "kraken_out",
overwrite = FALSE,
runner = GetDefaultBascetRunner(),
bascetInstance = GetDefaultBascetInstance()
)Arguments
- bascetRoot
The root folder where all Bascets are stored
- useKrakenDB
Path to KRAKEN2 database
- numLocalThreads
Number of threads for one KRAKEN instance
- inputName
Name of input shard (FASTQ)
- outputName
Name of output shard (kraken data)
- overwrite
Force overwriting of existing files. The default is to do nothing files exist
- runner
The job manager, specifying how the command will be run (e.g. locally, or via SLURM)
- bascetInstance
A Bascet instance