* Update README
* Rename pytest_software.yml to pytest_modules.yml
* Rename main software directory to modules
* Remove deprecated modules
* Rename tests software to modules
* Replace paths for tests in pytest_modules.yml
* Replace software with modules in Github Actions
* Replace software with modules in main.nf tests
* Rename software to modules in test.yml
* Update salmon/quant to provide '--libType A' option
* Modify lib_type description to be a string
* Update tests
* lyb_type can be explicitly overwrite
* Update main.nf
* Update main.nf
* Update main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>