Tool Object

Base R6 class for all nemo tools. Subclasses implement parsers for specific bioinformatic tool outputs by optionally overriding parse_{table_name}() and tidy_{table_name}() methods for custom parse or tidy logic per table.

A Tool object:

has a name (name);
has a path to a directory with its outputs (path);
has a schema configuration Config object (config);
exposes matched files via list_files();
exposes parsed and tidied tables via get_tbls();

The typical workflow is: optionally filter files with filter_files(), parse and tidy with tidy(), then write outputs with write(). run() chains all three steps.

Public fields

name: (character(1))
Name of tool.
pkg: (character(1))
Package name tool belongs to (for config lookup).
path: (character(1))
Output directory of tool.
config: (Config())
Config of tool.
written_files: (tibble())
Tibble of files written from self$write().

Methods

Method `new()`

Create a new Tool object.

Usage

Tool$new(name, pkg, path = NULL, files_tbl = NULL)

Arguments

name: (character(1))
Name of tool.
pkg: (character(1))
Package name tool belongs to (for config lookup).
path: (character(1))
Output directory of tool. If files_tbl is supplied, this is ignored.
files_tbl: (tibble(n))
Tibble of files from list_files_dir().

Returns

(R6::R6Class())
R6 object.

Method `print()`

Print details about the Tool.

Usage

Tool$print(...)

Arguments

...: (ignored).

Returns

(R6::R6Class())
R6 object invisibly.

Method `list_files()`

List files matching this tool's patterns.

Usage

Tool$list_files()

Returns

(tibble())
The files tibble of matched files. Always a tibble (possibly zero-row), never NULL.

Method `get_tbls()`

Get tidy tibbles after parsing and tidying.

Usage

Tool$get_tbls()

Returns

(tibble() or NULL)
The tbls tibble, or NULL if tidy() has not been called or if tidy() found no matching files. When tidy(keep_raw = TRUE) was used, the tibble also contains a raw list-column of the unparsed tibbles.

Method `filter_files()`

Filter files in given tool directory based on inclusion or exclusion tool_parser names. The result is reflected in the files field.

Usage

Tool$filter_files(include = NULL, exclude = NULL)

Arguments

include: (character(n))
tool_parser names to include (e.g. "tool1_table1").
exclude: (character(n))
tool_parser names to exclude (e.g. "tool1_table3").

Returns

(R6::R6Class())
R6 object invisibly.

Method `tidy()`

Tidy a list of files. The result is reflected in the tbls field.

Usage

Tool$tidy(keep_raw = FALSE)

Arguments

keep_raw: (logical(1))
Should the raw parsed tibbles be kept in the final output?

Returns

(R6::R6Class())
R6 object invisibly.

Method `write()`

Write tidy tibbles.

Usage

Tool$write(
  output_dir = ".",
  format = "tsv",
  input_id = NULL,
  output_id = NULL,
  prefix_include = FALSE,
  dbconn = NULL,
  write_metadata = TRUE
)

Arguments

output_dir: (character(1))
Directory path to output tidy files. Ignored if format is db.
format: (character(1))
Format of output.
input_id: (character(1))
Input ID to use for the dataset (e.g. run123).
output_id: (character(1))
Output ID to use for the dataset (e.g. out1).
prefix_include: (logical(1))
If TRUE, prepend an input_prefix column to each tidy table.
dbconn: (DBIConnection)
Database connection object (see DBI::dbConnect).
write_metadata: (logical(1))
If TRUE (default), write a metadata_<tool>.parquet file alongside the tidy outputs. Set to FALSE when a Workflow is orchestrating the write and will emit its own workflow-level metadata instead.

Returns

(R6::R6Class())
R6 object invisibly. Results stored in self$written_files (NULL if no files were found).

Method `get_metadata()`

Get metadata for the tool run.

Usage

Tool$get_metadata(input_id, output_id, output_dir, pkgs = NULL)

Arguments

input_id: (character(1))
Input ID to use for the dataset (e.g. run123).
output_id: (character(1))
Output ID to use for the dataset (e.g. out1).
output_dir: (character(1))
Output directory.
pkgs: (character(n))
Which R packages to extract versions for.

Returns

(tibble())
Single-row tibble with columns input_id, output_id, input_dirs, output_dir, pkg_versions, and files.

Method `run()`

Filter, tidy, and write files in one step.

Usage

Tool$run(
  output_dir = ".",
  format = "tsv",
  input_id = NULL,
  output_id = NULL,
  prefix_include = FALSE,
  dbconn = NULL,
  write_metadata = TRUE,
  include = NULL,
  exclude = NULL
)

Arguments

output_dir: (character(1))
Directory path to output tidy files.
format: (character(1))
Format of output.
input_id: (character(1))
Input ID to use for the dataset (e.g. run123).
output_id: (character(1))
Output ID to use for the dataset (e.g. out1).
prefix_include: (logical(1))
If TRUE, prepend an input_prefix column to each tidy table.
dbconn: (DBIConnection)
Database connection object (see DBI::dbConnect).
write_metadata: (logical(1))
If TRUE (default), write a metadata_<tool>.parquet file alongside the tidy outputs. Set to FALSE to suppress.
include: (character(n))
tool_parser names to include (e.g. "tool1_table1").
exclude: (character(n))
tool_parser names to exclude (e.g. "tool1_table5").

Returns

(R6::R6Class())
R6 object invisibly. Results stored in self$written_files.

Examples

fs::path(tempdir(), letters[1:5]) |>
  fs::file_temp_push() |>
  fs::dir_create()
name <- "tool1"; pkg <- "nemo";
path <- system.file("extdata/tool1", package = "nemo")
toolA <- Tool$new(name = name, pkg = pkg, path = path)
toolA$list_files()
#> # A tibble: 12 × 9
#>    tool_parser  parser bname       size lastmodified        path  pattern prefix
#>    <chr>        <chr>  <chr>      <fs:> <dttm>              <chr> <chr>   <chr> 
#>  1 tool1_table1 table1 sampleA.t…   133 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  2 tool1_table1 table1 sampleA.t…   113 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  3 tool1_table1 table1 sampleA.t…    93 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  4 tool1_table2 table2 sampleA.t…    70 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  5 tool1_table2 table2 sampleA.t…    47 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  6 tool1_table3 table3 sampleA.t…    83 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  7 tool1_table3 table3 sampleA.t…    48 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  8 tool1_table4 table4 sampleA.t…    52 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  9 tool1_table4 table4 sampleA.t…    34 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#> 10 tool1_table6 table6 sampleA.t…   100 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#> 11 tool1_table6 table6 sampleA.t…    78 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#> 12 tool1_table5 table5 sampleA.t…   994 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#> # ℹ 1 more variable: prefix_suffix <chr>
toolA$filter_files(exclude = "tool1_table3"); toolA$list_files() # note the exclusion this time
#> # A tibble: 10 × 9
#>    tool_parser  parser bname       size lastmodified        path  pattern prefix
#>    <chr>        <chr>  <chr>      <fs:> <dttm>              <chr> <chr>   <chr> 
#>  1 tool1_table1 table1 sampleA.t…   133 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  2 tool1_table1 table1 sampleA.t…   113 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  3 tool1_table1 table1 sampleA.t…    93 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  4 tool1_table2 table2 sampleA.t…    70 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  5 tool1_table2 table2 sampleA.t…    47 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  6 tool1_table4 table4 sampleA.t…    52 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  7 tool1_table4 table4 sampleA.t…    34 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  8 tool1_table6 table6 sampleA.t…   100 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  9 tool1_table6 table6 sampleA.t…    78 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#> 10 tool1_table5 table5 sampleA.t…   994 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#> # ℹ 1 more variable: prefix_suffix <chr>

toolB <- Tool$new(name = name, pkg = pkg, path = path)$
  filter_files(include = "tool1_table1")
toolB$list_files()
#> # A tibble: 3 × 9
#>   tool_parser  parser bname        size lastmodified        path  pattern prefix
#>   <chr>        <chr>  <chr>       <fs:> <dttm>              <chr> <chr>   <chr> 
#> 1 tool1_table1 table1 sampleA.to…   133 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#> 2 tool1_table1 table1 sampleA.to…   113 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#> 3 tool1_table1 table1 sampleA.to…    93 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#> # ℹ 1 more variable: prefix_suffix <chr>
# tidy + write
toolC <- Tool$new(name = name, pkg = pkg, path = path)$
  filter_files(exclude = "tool1_table5")$
  tidy()
toolC$list_files()
#> # A tibble: 11 × 9
#>    tool_parser  parser bname       size lastmodified        path  pattern prefix
#>    <chr>        <chr>  <chr>      <fs:> <dttm>              <chr> <chr>   <chr> 
#>  1 tool1_table1 table1 sampleA.t…   133 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  2 tool1_table1 table1 sampleA.t…   113 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  3 tool1_table1 table1 sampleA.t…    93 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  4 tool1_table2 table2 sampleA.t…    70 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  5 tool1_table2 table2 sampleA.t…    47 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  6 tool1_table3 table3 sampleA.t…    83 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  7 tool1_table3 table3 sampleA.t…    48 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  8 tool1_table4 table4 sampleA.t…    52 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  9 tool1_table4 table4 sampleA.t…    34 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#> 10 tool1_table6 table6 sampleA.t…   100 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#> 11 tool1_table6 table6 sampleA.t…    78 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#> # ℹ 1 more variable: prefix_suffix <chr>
toolC$get_tbls() # note the tidy column
#> # A tibble: 11 × 10
#>    tool_parser  parser bname       size lastmodified        path  pattern prefix
#>    <chr>        <chr>  <chr>      <fs:> <dttm>              <chr> <chr>   <chr> 
#>  1 tool1_table1 table1 sampleA.t…   133 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  2 tool1_table1 table1 sampleA.t…   113 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  3 tool1_table1 table1 sampleA.t…    93 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  4 tool1_table2 table2 sampleA.t…    70 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  5 tool1_table2 table2 sampleA.t…    47 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  6 tool1_table3 table3 sampleA.t…    83 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  7 tool1_table3 table3 sampleA.t…    48 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  8 tool1_table4 table4 sampleA.t…    52 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#>  9 tool1_table4 table4 sampleA.t…    34 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#> 10 tool1_table6 table6 sampleA.t…   100 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#> 11 tool1_table6 table6 sampleA.t…    78 2026-07-28 09:30:14 /hom… "\\.to… sampl…
#> # ℹ 2 more variables: prefix_suffix <chr>, tidy <list>
dir1 <- fs::file_temp(); dir2 <- fs::file_temp()
toolC$write(output_dir = dir1, format = "parquet", input_id = "run1")
(lfC <- list.files(dir1, full.names = TRUE))
#>  [1] "/tmp/RtmpLFaYvY/a/metadata_tool1.parquet"        
#>  [2] "/tmp/RtmpLFaYvY/a/sampleA_2_tool1_table1.parquet"
#>  [3] "/tmp/RtmpLFaYvY/a/sampleA_2_tool1_table2.parquet"
#>  [4] "/tmp/RtmpLFaYvY/a/sampleA_2_tool1_table3.parquet"
#>  [5] "/tmp/RtmpLFaYvY/a/sampleA_2_tool1_table4.parquet"
#>  [6] "/tmp/RtmpLFaYvY/a/sampleA_2_tool1_table6.parquet"
#>  [7] "/tmp/RtmpLFaYvY/a/sampleA_3_tool1_table1.parquet"
#>  [8] "/tmp/RtmpLFaYvY/a/sampleA_tool1_table1.parquet"  
#>  [9] "/tmp/RtmpLFaYvY/a/sampleA_tool1_table2.parquet"  
#> [10] "/tmp/RtmpLFaYvY/a/sampleA_tool1_table3.parquet"  
#> [11] "/tmp/RtmpLFaYvY/a/sampleA_tool1_table4.parquet"  
#> [12] "/tmp/RtmpLFaYvY/a/sampleA_tool1_table6.parquet"  

# run
toolD <- Tool$new(name = name, pkg = pkg, path = path)$
  filter_files(exclude = "tool1_table5")$
  run(output_dir = dir2, format = "parquet", input_id = "run2")
(lfD <- list.files(dir2, full.names = TRUE))
#>  [1] "/tmp/RtmpLFaYvY/b/metadata_tool1.parquet"        
#>  [2] "/tmp/RtmpLFaYvY/b/sampleA_2_tool1_table1.parquet"
#>  [3] "/tmp/RtmpLFaYvY/b/sampleA_2_tool1_table2.parquet"
#>  [4] "/tmp/RtmpLFaYvY/b/sampleA_2_tool1_table3.parquet"
#>  [5] "/tmp/RtmpLFaYvY/b/sampleA_2_tool1_table4.parquet"
#>  [6] "/tmp/RtmpLFaYvY/b/sampleA_2_tool1_table6.parquet"
#>  [7] "/tmp/RtmpLFaYvY/b/sampleA_3_tool1_table1.parquet"
#>  [8] "/tmp/RtmpLFaYvY/b/sampleA_tool1_table1.parquet"  
#>  [9] "/tmp/RtmpLFaYvY/b/sampleA_tool1_table2.parquet"  
#> [10] "/tmp/RtmpLFaYvY/b/sampleA_tool1_table3.parquet"  
#> [11] "/tmp/RtmpLFaYvY/b/sampleA_tool1_table4.parquet"  
#> [12] "/tmp/RtmpLFaYvY/b/sampleA_tool1_table6.parquet"

Public fields

Methods

Public methods

Method new()

Usage

Arguments

Returns

Method print()

Usage

Arguments

Returns

Method list_files()

Usage

Returns

Method get_tbls()

Usage

Returns

Method filter_files()

Usage

Arguments

Returns

Method tidy()

Usage

Arguments

Returns

Method write()

Usage

Arguments

Returns

Method get_metadata()

Usage

Arguments

Returns

Method run()

Usage

Arguments

Returns

Examples

Method `new()`

Method `print()`

Method `list_files()`

Method `get_tbls()`

Method `filter_files()`

Method `tidy()`

Method `write()`

Method `get_metadata()`

Method `run()`