CONTRIBUTING.md

In roryk/bcbioRnaseq: RNA-Seq Utilities

Contributing to bcbioRNASeq development

• For all changes, fork or create a new branch, then issue a pull request that will be reviewed.
• Do not commit changes directly to master branch.
• Open issues for any changes affecting bcbioRNASeq class.
• Support is only provided for the current release version.

Package style syntax

Attempt to follow these style guides, by priority: (1) Bioconductor coding style; (2) tidyverse style guide; (3) Google R style guide.

• Object and function parameter arguments should be formated in lowerCamelCase.
• Use spaces instead of tabs. Indent with 4 spaces.
• Use <- and not = for assignment.
• Explicitly define if/then statements using opening and closing brackets ({, }).
• else declarations should be on the same line as the closing bracket.
• Use spaces around assignment operators (<-), brackets ({), and comma delimiters (e.g. c("foo", "bar") not c("foo","bar").

Required checks

If there are changes to bcbioRNASeq class or loadRNASeq() function, be sure to rebuild all working example data:

source(file.path("data-raw", "examples.R"))

For all package updates, run these commands prior to a pull request:

lintr::lint_package()
devtools::document()
devtools::run_examples()
devtools::test()
devtools::check()
BiocCheck::BiocCheck(getwd())

Rebuild website

unlink("docs", recursive = TRUE)
pkgdown::build_site()

Beside this, the package should be able to run the templates. This should be done in the parent directory of bcbioRNASeq folder.

git clone https://github.com/bcbio/bcbio_rnaseq_output_example.git
cd bcbio_rnaseq_output_example
Rscript -e 'testthat::test_file("test_reports.R")'

Make sure qc.html and de.html are created inside reports folder and the figures and tables look as expected.

roryk/bcbioRnaseq documentation built on May 27, 2019, 10:44 p.m.