Package: nfcore.utils 0.0.4
Louis Le Nezet
nfcore.utils: Utilities for 'nf-core' Modules
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>.
Authors:
nfcore.utils_0.0.4.tar.gz
nfcore.utils_0.0.4.tar.gz(r-4.7-any)nfcore.utils_0.0.4.tar.gz(r-4.6-any)
nfcore.utils_0.0.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
nfcore.utils/json (API)
NEWS
| # Install 'nfcore.utils' in R: |
| install.packages('nfcore.utils', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/nf-core/r-nf-core-utils/issues
Last updated from:d69f36ca06. Checks:4 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 115 | ||
| source / vignettes | OK | 140 | ||
| linux-release-x86_64 | OK | 117 | ||
| wasm-release | OK | 96 |
Exports:create_log_session_infocreate_versions_ymlis_null_or_invalidis_valid_stringnullifyparse_argumentsprocess_endprocess_inputsvalid_stringvalidate_booleanvalidate_doublevalidate_filevalidate_foldervalidate_integer
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| The nf-core utils R package for Nextflow processes | nfcore.utils-package nfcore.utils |
| Log R session info | create_log_session_info |
| Create versions.yml file | create_versions_yml |
| Check if is 'NULL' or invalid | is_null_or_invalid |
| Check for Non-Empty, Non-Whitespace String | is_valid_string |
| Turn “null” or empty strings into actual NULL | nullify |
| Parse out options from a string without recourse to optparse | parse_arguments |
| Process end of the workflow | process_end |
| Process input parameters and files | process_inputs |
| Flexibly read CSV or TSV files | read_delim_flexible |
| Check for Non-Empty, Non-Whitespace String | valid_string |
| Check if value is a boolean | validate_boolean |
| Check if value is a double number | validate_double |
| Check if value is an existing file | validate_file |
| Check if value is an existing folder | validate_folder |
| Check if value is an integer | validate_integer |
