Dependency image refactor

[Taepper]

Summary

Test whether we can omit one dependency image. This is required to run our unit tests in debug mode, which is advised.

PR Checklist

• All necessary documentation has been adapted or there is an issue to do so.
• The implemented feature is covered by an appropriate test.

[github-actions]

This is a preview of the changelog of the next release. If this branch is not up-to-date with the current main branch, the changelog may not be accurate. Rebase your branch on the main branch to get the most accurate changelog.

Note that this might contain changes that are on main, but not yet released.

Changelog:

0.4.0 (2024-11-14)

⚠ BREAKING CHANGES

• metadataInputFile key in preprocessing config file has been removed. Instead, ndjson files should be used and specified with the ndjsonInputFilename option

Features

• remove tsv/fasta/sam input format (#562) (fd7dc6f)

Bug Fixes

• preprocessing: correct error message when field is in config but not in metadata file (828182a)
• remove shared_ptr in lambda captures which might lead to memory leaks (a26d8b8)