After a meeting today, Steven and Hollie realized that the Bismark coverage files were still using the old scaffold names, stemming from the Pgenerosa_v074 naming. I’d previously updated filenames and scaffold names, so I recycled some of the code used there to rename the coverage files.
The renaming was done in the following Jupyter Notebook (GitHub):
All files have also been uploaded to the
bismark_coverage_files folder in the OSF repository for this project.