Start workflowr project.

.Rprofile

+## This makes sure that R loads the workflowr package
+## automatically, everytime the project is loaded
+if (requireNamespace("workflowr", quietly = TRUE)) {
+  message("Loading .Rprofile for the current workflowr project")
+  library("workflowr")
+} else {
+  message("workflowr package not installed, please run install.packages(\"workflowr\") to use the workflowr functions")
+}

.gitattributes

+# Classify R Markdown files as R code for GitHub language statistics
+# https://github.com/github/linguist#overrides
+*.[Rr]md linguist-language=R

.gitignore

+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+.Rapp.history
+.DS_Store
+analysis/figure
+analysis/*png
+analysis/*html
+analysis/*_cache
+analysis/site_libs

README.md

+# chipseq-pipeline
+
+A [workflowr][] project.
+
+[workflowr]: https://github.com/workflowr/workflowr

_workflowr.yml

+# workflowr options
+# Version 1.7.0
+
+# The seed to use for random number generation. See ?set.seed for details.
+seed: 20220209
+# The working directory to build the R Markdown files. The path is relative to
+# _workflowr.yml. See ?rmarkdown::render for details.
+knit_root_dir: "."

analysis/_site.yml

+name: "chipseq-pipeline"
+output_dir: ../docs
+navbar:
+  title: "chipseq-pipeline"
+  left:
+  - text: Home
+    href: index.html
+  - text: About
+    href: about.html
+  - text: License
+    href: license.html
+output:
+  workflowr::wflow_html:
+    toc: yes
+    toc_float: yes
+    theme: cosmo
+    highlight: textmate

analysis/about.Rmd

+---
+title: "About"
+output:
+  workflowr::wflow_html:
+    toc: false
+editor_options:
+  chunk_output_type: console
+---
+
+Describe your project.

analysis/index.Rmd

+---
+title: "Home"
+site: workflowr::wflow_site
+output:
+  workflowr::wflow_html:
+    toc: false
+editor_options:
+  chunk_output_type: console
+---
+
+Welcome to my research website.

analysis/license.Rmd

+---
+title: "License"
+output:
+  workflowr::wflow_html:
+    toc: false
+editor_options:
+  chunk_output_type: console
+---
+
+What license are you using for your code? See [choosealicense.com][choose] for
+help deciding. It's a convention to save a file `LICENSE` in the root of your
+Git repo that contains the license text.
+
+What license are you using for the written content on your site? It is
+traditional to choose a [Creative Commons][cc] license for this type of content.
+
+[choose]: https://choosealicense.com/
+[cc]: https://creativecommons.org/choose/
+
+How should others cite your work? It's a convention to save a file `CITATION`
+in the root of your Git repo that contains the citation information.

chipseq-pipeline.Rproj

+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: Yes
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes

code/README.md

+# Code
+
+Save command-line scripts and shared R code here.

data/README.md

+# Data
+
+Save raw data files here.

output/README.md

+# Output
+
+Save processed data files here.