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Workflow Object

Source: R/Workflow.R
Workflow.Rd

A Workflow is composed of multiple Tools.

Public fields

name

(character(1))
Name of workflow.

path

(character(n))
Path(s) to workflow results.

tools

(list(n))
List of Tools that compose a Workflow.

files_tbl

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

written_files

(tibble(n))
Tibble of files written from self$write().

Methods

Public methods

Method new()

Create a new Workflow object.

Usage

Workflow$new(name = NULL, path = NULL, tools = NULL)

Arguments

name

(character(1))
Name of workflow.

path

(character(n))
Path(s) to workflow results.

tools

(list(n))
List of Tools that compose a Workflow.

Method print()

Print details about the File.

Usage

Workflow$print(...)

Arguments

...

(ignored).

Method filter_files()

Filter files in given workflow directory.

Usage

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

Arguments

include

(character(n))
Files to include.

exclude

(character(n))
Files to exclude.

Method list_files()

List files in given workflow directory.

Usage

Workflow$list_files(type = c("file", "symlink"))

Arguments

type

(character(1))
File types(s) to return (e.g. any, file, directory, symlink). See fs::dir_info.

Returns

A tibble with all files found for each Tool.

Method tidy()

Tidy Workflow files.

Usage

Workflow$tidy(tidy = TRUE, keep_raw = FALSE)

Arguments

tidy

(logical(1))
Should the raw parsed tibbles get tidied?

keep_raw

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

Returns

self invisibly.

Method write()

Write tidy tibbles.

Usage

Workflow$write(
  diro = ".",
  format = "tsv",
  input_id = NULL,
  output_id = ulid::ulid(),
  dbconn = NULL
)

Arguments

diro

(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. run123).

dbconn

(DBIConnection)
Database connection object (see DBI::dbConnect).

Returns

self invisibly.

Method nemofy()

Parse, filter, tidy and write files.

Usage

Workflow$nemofy(
  diro = ".",
  format = "tsv",
  input_id = NULL,
  output_id = ulid::ulid(),
  dbconn = NULL,
  include = NULL,
  exclude = NULL
)

Arguments

diro

(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. run123).

dbconn

(DBIConnection)
Database connection object (see DBI::dbConnect).

include

(character(n))
Files to include.

exclude

(character(n))
Files to exclude.

Returns

self invisibly.

Method get_raw_schemas_all()

Get raw schemas for all Tools.

Usage

Workflow$get_raw_schemas_all()

Returns

Tibble with names of tool and file, schema and its version.

Method get_tidy_schemas_all()

Get tidy schemas for all Tools.

Usage

Workflow$get_tidy_schemas_all()

Returns

Tibble with names of tool and tbl, schema and its version.

Method get_tbls()

Get tidy tbls for all Tools.

Usage

Workflow$get_tbls()

Returns

Tibble with tidy tbls of all Tools.

Method get_metadata()

Get metadata

Usage

Workflow$get_metadata(input_id, output_id, output_dir, pkgs = c("nemo"))

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. run123).

output_dir

(character(1))
Output directory.

pkgs

(character(n))
Which R packages to extract versions for.

Returns

List with metadata

Method clone()

The objects of this class are cloneable with this method.

Usage

Workflow$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

path <- system.file("extdata/tool1", package = "nemo")
tools <- list(tool1 = Tool1)
wf1 <- Workflow$new(name = "foo", path = path, tools = tools)
diro <- tempdir()
wf1$list_files()
#> # A tibble: 4 × 9
#>   tool_parser  parser bname  size lastmodified        path  pattern prefix group
#>   <glue>       <chr>  <chr> <fs:> <dttm>              <chr> <chr>   <glue> <glu>
#> 1 tool1_table1 table1 samp…   113 2026-02-08 23:24:37 /hom… "\\.to… sampl…      
#> 2 tool1_table1 table1 samp…   153 2026-02-08 23:24:37 /hom… "\\.to… sampl… _2   
#> 3 tool1_table2 table2 samp…    70 2026-02-08 23:24:37 /hom… "\\.to… sampl…      
#> 4 tool1_table3 table3 samp…    83 2026-02-08 23:24:37 /hom… "\\.to… sampl…      
wf1$nemofy(diro = diro, format = "parquet", input_id = "run1")
(lf <- list.files(diro, pattern = "tool1.*parquet", full.names = FALSE))
#> [1] "sampleA_2_tool1_table1.parquet" "sampleA_tool1_table1.parquet"  
#> [3] "sampleA_tool1_table2.parquet"   "sampleA_tool1_table3.parquet"  
#dbconn <- DBI::dbConnect(drv = RPostgres::Postgres(), dbname = "nemo", user = "orcabus")
#wf1$nemofy(format = "db", id = "runABC", dbconn = dbconn)