Calls minimap2 to index the reference genome.
Value
A SummarizedExperiment
object, a SingleCellExperiment
object,
or a list of SingleCellExperiment
objects.
Examples
pipeline <- example_pipeline(type = "BulkPipeline")
#> Writing configuration parameters to: /tmp/RtmpyvgB0f/file76e31a610a9f/config_file_30435.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)