Package {nfcore.utils}

Version:	0.0.4
Date:	2026-06-17
Title:	Utilities for 'nf-core' Modules
Depends:	R (≥ 4.4.0),
Imports:	utils
Description:	Provides utility functions to facilitate the use of R within nf-core modules. The package helps parse 'Nextflow' inputs and perform validation checks to ensure correct parameter handling and reproducible execution. For more details see Ewels (2020) <doi:10.1038/s41587-020-0439-x>.
License:	MIT + file LICENSE
Encoding:	UTF-8
RoxygenNote:	7.3.3
VignetteBuilder:	knitr
Suggests:	testthat (≥ 3.0.0), rmarkdown, BiocStyle, knitr, withr, yaml
Config/testthat/edition:	3
BugReports:	https://github.com/nf-core/r-nf-core-utils/issues
URL:	https://github.com/nf-core/r-nf-core-utils
NeedsCompilation:	no
Packaged:	2026-06-17 10:25:41 UTC; llenezet
Author:	nf-core Community [aut], Louis Le Nezet [aut, cre, cph]
Maintainer:	Louis Le Nezet <louislenezet@gmail.com>
Repository:	CRAN
Date/Publication:	2026-06-22 15:10:02 UTC

The nf-core utils R package for Nextflow processes

Description

This package aims to ease the link between Nextflow inputs and outputs to the R variable needed in the script.

Functions

Below are listed some of the main functions available:

process_inputs(): Given a list of expected options with their default this function will parse the arguments given and validate their value based on the expected rules.

process_end(): Create a versions.yml and R_sessionInfo.log file in the directory provided. The version file will be populated with the R version, the version of nfcore.utils and the version of the additional packages given.

Author(s)

Maintainer: Louis Le Nezet louislenezet@gmail.com (ORCID) [copyright holder]

Authors:

• nf-core Community

See Also

Useful links:

• https://github.com/nf-core/r-nf-core-utils

• Report bugs at https://github.com/nf-core/r-nf-core-utils/issues

Examples

library(nfcore.utils)
td <- withr::local_tempdir()
test_file_path <- file.path(td, "test_file.txt")
file.create(test_file_path)
my_options <- list(
  input_file = test_file_path,
  output_file = "prefix",
  threshold = 0.5
)
args <- c("--threshold 0.7")
processed_options <- process_inputs(
  my_options, args,
  keys_to_nullify = c("input_file", "output_file"),
  expected_files = c("input_file"),
  expected_double = c("threshold"),
  required_opts = c("input_file", "threshold")
)
## Not run: 
process_end(
  packages = list(
    "r-stats" = "stats"
  ),
  task_name = 'MY_PROCESS'
)

## End(Not run)

Log R session info

Description

This function logs the R session info to a file named R_sessionInfo.log in the specified output directory.

Usage

create_log_session_info(log_path = "R_sessionInfo.log")

Arguments

Value

R session info log

Examples

td <- withr::local_tempdir()
create_log_session_info(file.path(td, "session.log"))

Create versions.yml file

Description

This function allows to automatically create the versions.yml file used to store the packages used. r-base as well as r-nfcore.utils versions will automatically be added.

Usage

create_versions_yml(packages, task_name, versions_path = "versions.yml")

Arguments

Value

versions.yml file

Examples

td <- withr::local_tempdir()
create_versions_yml(
  list("r-stats" = "stats"), "MY_PROCESS",
  file.path(td, "my_versions.yml")
)

Check if is NULL or invalid

Description

Check if is NULL or invalid

Usage

is_null_or_invalid(x, variable_name = NULL)

Arguments

Value

TRUE if is null, ERROR if invalid and FALSE otherwise

Examples

is_null_or_invalid(NULL) # TRUE
try(is_null_or_invalid(" ")) # ERROR
is_null_or_invalid("Hello World !") # FALSE

Check for Non-Empty, Non-Whitespace String

Description

This function checks if the input is non-NULL and contains more than just whitespace. It returns TRUE if the input is a non-empty, non-whitespace string, and FALSE otherwise.

Usage

is_valid_string(input)

Arguments

Value

A logical value: TRUE if the input is a valid, non-empty, non-whitespace string; FALSE otherwise.

Examples

is_valid_string("Hello World") # Returns TRUE
is_valid_string(" Hello World ") # Returns TRUE
is_valid_string("   ")         # Returns FALSE
is_valid_string(NULL)          # Returns FALSE

Turn “null” or empty strings into actual NULL

Description

Turn “null” or empty strings into actual NULL

Usage

nullify(x)

Arguments

Value

NULL or x

Examples

nullify("null") # Returns NULL
nullify("NULL") # Returns NULL
nullify("   ")  # Returns NULL
nullify("")     # Returns NULL
nullify(NULL)   # Returns NULL
nullify(NA)     # Returns NULL
nullify("Hello") # Returns "Hello"

Parse out options from a string without recourse to optparse

Description

If only the key is given, the value will be set to TRUE

Usage

parse_arguments(x)

Arguments

Value

named list of options and values similar to optparse

Examples

parse_arguments("--opt1 val1 --opt2 val2")
parse_arguments(' --opt1-extra "value with space" --opt2 val2 ')

Process end of the workflow

Description

Create the versions.yml file and log session info at the end of the process.

Usage

process_end(
  packages,
  task_name,
  versions_path = "versions.yml",
  log_path = "R_sessionInfo.log"
)

Arguments

Value

versions.yml file and R session info log

Examples

td <- withr::local_tempdir()
process_end(
  list("r-stats" = "stats"),
  "MY_PROCESS",
  file.path(td, "my_versions.yml"),
  file.path(td, "session.log")
)

Process input parameters and files

Description

This function processes input parameters and files, applying parameter overrides, validating expected keys and files, and ensuring that the provided file paths are valid.

Usage

process_inputs(
  opt,
  args = NULL,
  keys_to_nullify = NULL,
  expected_files = NULL,
  expected_folders = NULL,
  expected_double = NULL,
  expected_integer = NULL,
  expected_boolean = NULL,
  required_opts = NULL
)

Arguments

Value

A list of processed options with overrides applied and validated.

Examples

td <- withr::local_tempdir()
test_file_path <- file.path(td, "test_file.txt")
file.create(test_file_path)
my_options <- list(
  input_file = test_file_path,
  output_file = "prefix",
  threshold = 0.5,
  "is-a-test" = NULL
)
args <- c("--threshold 0.7 --is-a-test")
processed_options <- process_inputs(
  my_options, args,
  keys_to_nullify = c("input_file", "output_file"),
  expected_files = c("input_file"),
  expected_double = c("threshold"),
  expected_boolean = c("is-a-test"),
  required_opts = c("input_file", "threshold")
)

Flexibly read CSV or TSV files

Description

The following rules are applied:

• extension == txt or tsv, then separator is set to tabulation

• extension == csv, then separator is set to comma

Usage

read_delim_flexible(file, ...)

Arguments

Value

output Data frame

Check for Non-Empty, Non-Whitespace String

Description

This function checks if the input is non-NULL and contains more than just whitespace.

Usage

valid_string(input)

Arguments

Value

input with whitespace trimmed or throw error if not a valid string

Examples

valid_string("Hello World") # Returns "Hello World"
valid_string("  Hello World ") # Returns "Hello World"
try(valid_string("   ")) # Error
try(valid_string(NULL)) # Error

Check if value is a boolean

Description

Convert to TRUE or FALSE with accepted lowered values as:

• TRUE: 1, yes, true

• FALSE: 0, no, false

Usage

validate_boolean(x, variable_name = NULL)

Arguments

Value

x as TRUE/FALSE, or NULL if is null and ERROR if x isn't convertable to a boolean

Examples

validate_boolean(NULL) # NULL
try(validate_boolean(" ")) # ERROR
try(validate_boolean("Hello World !")) # ERROR
try(validate_boolean(12.4)) # ERROR
validate_boolean("1") # TRUE
validate_boolean(0) # FALSE

Check if value is a double number

Description

Check if value is a double number

Usage

validate_double(x, variable_name = NULL)

Arguments

Value

x as double, or NULL if is null and ERROR if x isn't convertable to a double

Examples

validate_double(NULL) # NULL
try(validate_double(" ")) # ERROR
try(validate_double("Hello World !")) # ERROR
validate_double("12.4") # 12.4
validate_double("12") # 12.0

Check if value is an existing file

Description

Check if value is an existing file

Usage

validate_file(x, variable_name = NULL)

Arguments

Value

x, or NULL if is null and ERROR if x isn't an existing file

Examples

try(validate_file("test")) # ERROR

Check if value is an existing folder

Description

Check if value is an existing folder

Usage

validate_folder(x, variable_name = NULL)

Arguments

Value

x, or NULL if is null and ERROR if x isn't an existing folder

Examples

try(validate_folder("test")) # ERROR

Check if value is an integer

Description

Check if value is an integer

Usage

validate_integer(x, variable_name = NULL)

Arguments

Value

x as integer, or NULL if is null and ERROR if x isn't convertable to an integer

Examples

validate_integer(NULL) # NULL
try(validate_integer(" ")) # ERROR
try(validate_integer("Hello World !")) # ERROR
try(validate_integer("12.4")) # ERROR
validate_integer("12") # 12