First attempt to bring some of the nice scripts from Etienne to scilpy.
I choose to reduce the scope of the original script to fit scilpy requirements
I kept the expected behavior of the script used in nf-set.
...
Type of change
Check the relevant options.
[ ] Bug fix (non-breaking change which fixes an issue)
[x] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
[ ] This change requires a documentation update
Provide data, screenshots, command line to test (if relevant)
Use scilpy atlas test data
...
Checklist
[ ] My code follows the style guidelines of this project (run autopep8)
[ ] I added relevant citations to scripts, modules and functions docstrings and descriptions
[ ] I have performed a self-review of my code
[ ] I have commented my code, particularly in hard-to-understand areas
[ ] I have made corresponding changes to the documentation
[ ] My changes generate no new warnings
[ ] I moved all functions from the script file (except the argparser and main) to scilpy modules
[ ] I have added tests that prove my fix is effective or that my feature works
[ ] New and existing unit tests pass locally with my changes
Quick description
First attempt to bring some of the nice scripts from Etienne to scilpy. I choose to reduce the scope of the original script to fit scilpy requirements I kept the expected behavior of the script used in nf-set.
...
Type of change
Check the relevant options.
Provide data, screenshots, command line to test (if relevant)
Use scilpy atlas test data ...
Checklist