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Develop #310

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Develop #310

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siebrenf and others added 23 commits January 11, 2023 13:47
* Use .annotation_bed_file attribute of Genome

Use the `.annotation_bed_file attribute` instead of hardcoded `.fa` to `.bed.gz` replacement which does not work when only a non-zipped annotation file is available

* Update denovo.py

Remove unused variable
* update dependencies

* -e
* drop NO ORTHOLOGS FOUND from maelstrom report when redundant

* revert spaces between TFs

* format extra_str the same

* update changelog
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