* 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 test for trimgalore
* Fix picard markduplicate test
* Fix tests for picard mergesamfiles
* Fix checksum for markduplicates
* Fix multiplemetrics and wgsmetrics
* Fix checksum for mergesamfiles