The workflow still had a problem concerning the include flag. The output from get_assemblies_for_submission is a path, not a name, leading to a KeyError in get_include_flag in the common.smk. This way, all sequences are included in the report, also the ones with an initial include flag of 0.
## Related Issue
Description
The workflow still had a problem concerning the include flag. The output from get_assemblies_for_submission is a path, not a name, leading to a KeyError in get_include_flag in the common.smk. This way, all sequences are included in the report, also the ones with an initial include flag of 0. ## Related IssueChecklist
pre-commit
if needed.CODE_OF_CONDUCT.md
document.CONTRIBUTING.md
guide.