## ----global_options, include=FALSE-------------------------------------------- knitr::opts_chunk$set(fig.pos = 'h') doc_dir <- getwd() ## run all code in a temporary directory knitr::opts_knit$set(root.dir = tempdir()) ## ----packageInstallation, eval = FALSE---------------------------------------- # if (!"BiocManager" %in% rownames(installed.packages())) # install.packages("BiocManager") # BiocManager::install("BiocWorkflowTools") ## ----createBiocWorkflow, message=FALSE---------------------------------------- workflow_location <- file.path(tempdir(), "MyWorkflow") BiocWorkflowTools::createBiocWorkflow(path = workflow_location, open = FALSE) ## ----RStudioNew, echo = FALSE, out.width='50%', fig.align='center', fig.cap="Creation of a new article is integrated into RStudio. The F1000Research template can be accessed via the `New R Markdown' file menu dialog"---- knitr::include_graphics("figures/Rstudio_newdoc.png", error = FALSE) ## ----createDraft-------------------------------------------------------------- rmd_file <- rmarkdown::draft("MyArticle.Rmd", template = "f1000_article", package = "BiocWorkflowTools", edit = FALSE) ## ----render, eval = FALSE----------------------------------------------------- # rmarkdown::render(rmd_file) ## ----renderquiet, include = FALSE--------------------------------------------- rmarkdown::render(rmd_file, quiet=TRUE) ## ----uploadToOverleaf, eval=FALSE--------------------------------------------- # BiocWorkflowTools::uploadToOverleaf("MyArticle")