Index the reference genome for minimap2

Calls minimap2 to index the reference genome.

Usage

index_genome(pipeline, path, additional_args = c("-k", "14"))

# S4 method for class 'FLAMES.Pipeline'
index_genome(pipeline, path, additional_args = c("-k", "14"))

Arguments

pipeline

A FLAMES.Pipeline object.

path

The file path to save the minimap2 index. If not provided, it will be saved to the output directory with the name "genome.mmi".

additional_args

(optional) Additional arguments to pass to minimap2.

Value

A SummarizedExperiment object, a SingleCellExperiment object, or a list of SingleCellExperiment objects.

Examples

pipeline <- example_pipeline(type = "BulkPipeline")
#> Writing configuration parameters to:  /tmp/Rtmp3Wjsxa/file358a2f2c9953/config_file_13706.json 
#> Configured steps: 
#> 	genome_alignment: TRUE
#> 	isoform_identification: TRUE
#> 	read_realignment: TRUE
#> 	transcript_quantification: TRUE
#> samtools not found, will use Rsamtools package instead
pipeline <- index_genome(pipeline)