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Update README with v2.6 info and reorganise POM#155

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eladrion merged 3 commits intomainfrom
update_readme_to_2_6
Feb 11, 2026
Merged

Update README with v2.6 info and reorganise POM#155
eladrion merged 3 commits intomainfrom
update_readme_to_2_6

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@eladrion eladrion commented Feb 11, 2026

Pull Request Overview

This PR reorganises dependencies in POM (by blocking them) and documents missing mvnrepository URLs.
Also, the dependencies were updated in README.md. I checked and corrected all hrefs. Furthermore, added entry in manual download table for 2.6 and updated output formats (Snakemake and Shell scripts).

Related Issue

Changes Introduced

See above.

How Has This Been Tested?

Running mvn clean package which is sufficient since only the documentation was updated and the POM was reorganised.

Checklist

  • I have referenced a related issue.
  • I have followed the project’s style guidelines.
  • My changes include tests, if applicable.
  • All tests pass locally.
  • I have added myself to the CITATION.cff file, if not already present.

…URL. Also, update dependencies in README.md, check and correct all hrefs. Furthermore add entry in manual download table for 2.6 and update output formats.
@eladrion eladrion changed the title Update README with v2.6 into and reorganise POM Update README with v2.6 info and reorganise POM Feb 11, 2026
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@eladrion: Have to check whether the API description is actually still correct

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API description was outdated. Updated that.

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README fully updated. Merging

@eladrion eladrion merged commit 560b674 into main Feb 11, 2026
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@eladrion eladrion deleted the update_readme_to_2_6 branch February 11, 2026 16:05
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