This uses the bascet integrated fastqc command rather than the old mapcell system.
Usage
BascetMapCellFASTQC(
bascetRoot,
inputName = "filtered",
outputName = "fastqc",
numThreads = NULL,
numThreadsRead = NULL,
nogroup = FALSE,
expgroup = FALSE,
kmerSize = 7,
minLength = 0,
dupLength = 50,
maxReadsPerCell = 5e+06,
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
- numThreads
Total thread budget. Defaults to the runner CPU count
- numThreadsRead
Threads used by the TIRP reader. If NULL, use the CLI default
- nogroup
Do not group bases in the FastQC per-base modules
- expgroup
Use exponential base grouping in the FastQC per-base modules
- kmerSize
K-mer size for FastQC k-mer content
- minLength
Minimum sequence length to include
- dupLength
Length to truncate sequences for duplication detection
- maxReadsPerCell
Maximum read pairs per cell fed to FastQC. Defaults to 5e6 to bound memory for pathological high-read cells; NULL disables the cap. When a cell exceeds this, only the first N read pairs encountered in the file are used (no random subsampling)
- 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