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Last updated: 2019-12-05

Checks: 2 0

Knit directory: reproducible_bioinformatics/

This reproducible R Markdown analysis was created with workflowr (version 1.5.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Repository version: ec7204f

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:


Ignored files:
    Ignored:    .Rhistory

Unstaged changes:
    Modified:   analysis/_site.yml

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File	Version	Author	Date	Message
Rmd	ec7204f	davetang	2019-12-05	wflow_publish(files = c(“analysis/about.Rmd”, “analysis/conda.Rmd”, “analysis/docker.Rmd”,
html	2f6c2fd	Dave Tang	2019-12-05	Build site.
Rmd	f19271d	Dave Tang	2019-12-05	wflow_publish(files = c(“analysis/docker.Rmd”, “analysis/index.Rmd”))
html	7b114c5	First Last	2019-12-04	Build site.
Rmd	a4180a4	First Last	2019-12-04	wflow_publish(files = c(“analysis/conda.Rmd”, “analysis/index.Rmd”))
html	60a5900	First Last	2019-12-04	Build site.
html	d83e8cb	davetang	2019-12-03	Build site.
Rmd	88b592b	davetang	2019-12-03	New workflowr project
Rmd	4e0dfff	davetang	2019-12-03	Start workflowr project.

My aim for the workshop is to introduce computational tools and demonstrate how they can be used to help promote reproducibility when performing bioinformatic analyses. Many of these tools, especially workflowr help adhere to these Ten Simple Rules for Reproducible Computational Research: