TODO Should be managed by Bascet mapshard system, with automatic input conversion. unaligned file should be made temp and removed
Usage
BascetRunCellSNP(
bascetRoot,
inputName = "aligned",
outputName = "cellsnp",
numLocalThreads = NULL,
overwrite = FALSE,
runner = GetDefaultBascetRunner(),
bascetInstance = GetDefaultBascetInstance()
)Arguments
- bascetRoot
The root folder where all Bascets are stored
- inputName
Name of input shard
- outputName
Name of output shard
- numLocalThreads
Number of threads to use for each runner. Default is the maximum, taken from runner settings
- 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