DragenTool Object

Base class for the DRAGEN tools, adding the shared dragen-metrics ftype to nemo::Tool. A plain metrics table needs only ftype: 'dragen-metrics' in its schema; one needing normalise/drop_constant declares a tidy_<tbl>() that delegates to tidy_metrics().

Details

DRAGEN *_metrics.csv files are headerless section,rg,variable,count[,pct]. count is read as character (string values such as "XX", counts beyond 32-bit) and coerced to its schema type after the wide pivot.

Super class

nemo::Tool -> DragenTool

Public fields

on_unmapped

(character(1))
Policy for file metrics absent from the schema: error (default) or warn (drop them).

on_coerce_fail

(character(1))
Policy for a non-empty value that coerces to NA under its schema type: error (default) or warn (keep the NA).

on_unexpected_col

(character(1))
Policy for a drop_constant id column that varies across rows: error (default) or warn (keep the column).

Examples

# Abstract base: normally you use a subclass (e.g. DragenVar).
indir <- system.file("extdata/dragenmap", package = "tidydragen")
tool <- DragenTool$new(name = "dragenmap", pkg = "tidydragen", path = indir)
tool$list_files()      # inherited nemo::Tool file discovery
#> # A tibble: 11 × 9
#>    tool_parser     parser bname    size lastmodified        path  pattern prefix
#>    <chr>           <chr>  <chr> <fs::b> <dttm>              <chr> <chr>   <chr> 
#>  1 dragenmap_repl… replay samp…   3.94K 2026-10-24 07:30:33 /hom… "-repl… sampl…
#>  2 dragenmap_time  time   samp…     944 2026-10-24 07:30:33 /hom… "\\.ti… sampl…
#>  3 dragenmap_repl… replay samp…   2.44K 2026-10-24 07:30:33 /hom… "-repl… sampl…
#>  4 dragenmap_time  time   samp…      92 2026-10-24 07:30:33 /hom… "\\.ti… sampl…
#>  5 dragenmap_repl… replay samp…   1.82K 2026-10-24 07:30:33 /hom… "-repl… sampl…
#>  6 dragenmap_frag… fragl… samp…  19.39K 2026-10-24 07:30:33 /hom… "\\.fr… sampl…
#>  7 dragenmap_gc    gc     samp…  10.52K 2026-10-24 07:30:33 /hom… "\\.gc… sampl…
#>  8 dragenmap_metr… metri… samp…  27.03K 2026-10-24 07:30:33 /hom… "\\.ma… sampl…
#>  9 dragenmap_time  time   samp…    1.3K 2026-10-24 07:30:33 /hom… "\\.ti… sampl…
#> 10 dragenmap_trim… trimm… samp…   1.35K 2026-10-24 07:30:33 /hom… "\\.tr… sampl…
#> 11 dragenmap_umi   umi    samp…   5.22K 2026-10-24 07:30:33 /hom… "\\.um… sampl…
#> # ℹ 1 more variable: prefix_suffix <chr>
tool$on_unmapped       # "error": unmapped metrics abort rather than drop
#> [1] "error"
tool$on_coerce_fail    # "error": values that fail type coercion abort
#> [1] "error"

# flip a policy to be lenient (drop/keep-NA with a warning instead)
tool$on_unmapped <- "warn"

# fail-loud paths, via a corrupted copy of the DragenRna fixture
rna_dir <- system.file("extdata/dragenrna", package = "tidydragen")
bad_dir <- tempfile()
dir.create(bad_dir)
file.copy(list.files(rna_dir, full.names = TRUE), bad_dir)
#> [1] TRUE TRUE TRUE TRUE
qf <- file.path(bad_dir, "sampleA.quant_metrics.csv")
lines <- readLines(qf)