fix: fixed include flag KeyError

[AKBrueggemann]

Description

There was a problem with the include_flag in common.smk. The get_assemblies_for_submission function gives the path to the faster file, not the name, leading to a KeyError in get_include_flag. This causes the inclusion of files in the high-quality-genomes, that should be excluded. Problem fixed by changing the functions used in get_include_flag_for_date and taking into account the lengths of the lists from get_assemblies_for_submission and get_sample_for_date. ## Related Issue

Checklist

• [x] I've formatted the PR title in accordance with the structure of the conventional commit messages.
• [x] I've updated the code style using pre-commit if needed.
• [ ] I've updated or supplemented the documentation as needed.
• [x] I've read the CODE_OF_CONDUCT.md document.
• [x] I've read the CONTRIBUTING.md guide.