Extract barcodes and trim input raw FASTQ
Usage
BascetGetRaw(
bascetRoot,
rawmeta,
maxShardSize = "200g",
outputName = "debarcoded",
chemistry = c("atrandi-wgs", "atrandi-wgslr", "atrandi-rnaseq", "parse-bio"),
subchemistry = NULL,
barcodeTolerance = NULL,
numThreads = NULL,
numReadThreads = NULL,
numDebarcodeThreads = NULL,
numSortingThreads = NULL,
numMergeSortingThreads = NULL,
numWriteThreads = NULL,
numCompressThreads = NULL,
totalMem = NULL,
streamBufferSize = NULL,
sortBufferSize = NULL,
compressBufferSize = NULL,
compressRawBufferSize = NULL,
compressionLevel = NULL,
numMergeStreams = NULL,
overwrite = FALSE,
runner = GetDefaultBascetRunner(),
bascetInstance = GetDefaultBascetInstance()
)Arguments
- bascetRoot
The root folder where all Bascets are stored
- rawmeta
Metadata for the raw FASTQ input files. See DetectRawFileMeta
- maxShardSize
Estimated maximum size of output shard. Can be set higher but as sorting is also performed during sharding, it can be overall more efficient to only do partial sorting during this command
- outputName
Name output files: Debarcoded reads
- chemistry
The type of data to be parsed
- subchemistry
Sub-chemistry variant, if applicable
- barcodeTolerance
Optional: Number of mismatches allowed in the barcode for it to still be considered valid
- numThreads
Number of threads to use per job. Default is the number from the runner
- numReadThreads
Advanced setting: Number of threads for reading
- numDebarcodeThreads
Advanced setting: Number of threads for debarcoding
- numSortingThreads
Advanced setting: Number of threads for sorting, first phase
- numMergeSortingThreads
Advanced setting: Number of threads for sorting, second phase
- numWriteThreads
Advanced setting: Number of threads for writing
- numCompressThreads
Advanced setting: Number of threads for compressing
- totalMem
Total memory to allocate
- streamBufferSize
Advanced setting: Stream buffer size (fraction, given as e.g. "10%")
- sortBufferSize
Advanced setting: Sort buffer size (fraction, given as e.g. "10%")
- compressBufferSize
Advanced setting: Compress buffer size (fraction, given as e.g. "10%")
- compressRawBufferSize
Advanced setting: Raw compress buffer size (fraction, given as e.g. "10%")
- compressionLevel
Advanced setting: Compression level (0..12)
- numMergeStreams
Advanced setting: Number of merge streams (must be >= 2)
- 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