DragenBcl Object

Parses and tidies DRAGEN BCLConvert Reports/ outputs.

Super classes

nemo::Tool -> tidydragen::DragenTool -> DragenBcl

Methods

Public methods

• DragenBcl$new()

• DragenBcl$parse_demultiplexstats()

• DragenBcl$parse_demultiplextilestats()

• DragenBcl$parse_fastqlist()

• DragenBcl$parse_runinfo()

Inherited methods

• nemo::Tool$filter_files()
• nemo::Tool$get_globs()
• nemo::Tool$get_metadata()
• nemo::Tool$get_tbls()
• nemo::Tool$list_files()
• nemo::Tool$print()
• nemo::Tool$run()
• nemo::Tool$tidy()
• nemo::Tool$write()

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Method new()

Create a new DragenBcl object.

Usage

DragenBcl$new(path = NULL, files_tbl = NULL)

Arguments

path

(character(1))
Path to a BCLConvert Reports/ directory. If files_tbl is supplied, this is ignored.

files_tbl

(tibble(n))
Tibble of files from nemo::list_files_dir().

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Method parse_demultiplexstats()

Parse Demultiplex_Stats.csv.

Usage

DragenBcl$parse_demultiplexstats(x)

Arguments

x

(character(1))
Path to file.

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Method parse_demultiplextilestats()

Parse Demultiplex_Tile_Stats.csv.

Usage

DragenBcl$parse_demultiplextilestats(x)

Arguments

x

(character(1))
Path to file.

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Method parse_fastqlist()

Parse fastq_list.csv.

Usage

DragenBcl$parse_fastqlist(x)

Arguments

x

(character(1))
Path to file.

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Method parse_runinfo()

Parse RunInfo.xml.

Usage

DragenBcl$parse_runinfo(x)

Arguments

x

(character(1))
Path to file.

Examples

cls <- DragenBcl; tool <- "dragenbcl"
indir <- system.file("extdata", tool, package = "tidydragen")
odir <- tempdir()
obj <- cls$new(indir)
obj$run(output_dir = odir, format = "parquet", input_id = "run1", output_id = "out1")
(lf <- list.files(odir, pattern = "dragenbcl_.*parquet", full.names = FALSE))
#>  [1] "dragenbcl_adaptercyclemetrics.parquet" 
#>  [2] "dragenbcl_adaptermetrics.parquet"      
#>  [3] "dragenbcl_demultiplexstats.parquet"    
#>  [4] "dragenbcl_demultiplextilestats.parquet"
#>  [5] "dragenbcl_fastqlist.parquet"           
#>  [6] "dragenbcl_indexhoppingcounts.parquet"  
#>  [7] "dragenbcl_qualitymetrics.parquet"      
#>  [8] "dragenbcl_qualitytilemetrics.parquet"  
#>  [9] "dragenbcl_runinfo.parquet"             
#> [10] "dragenbcl_topunknownbarcodes.parquet"