Prepare release 54.4.0 - Githubissues

Checklist

[ ] Update CHANGELOG.rst for each commit separately:
- Pay attention to write entries under the "Unreleased" section.
- Mark all breaking changes as "BACKWARD INCOMPATIBLE:" and put them before non-breaking changes.
- If a commit modifies a feature listed under "Unreleased" section, it might be sufficient to modify the existing CHANGELOG entry from previous commit(s).
[ ] Bump the process version:
- MAJOR version (first number): Backward incompatible changes (changes that break the api/interface). Examples: renaming the input/output, adding mandatory input, removing input/output...
- MINOR version (middle number): add functionality or changes in a backwards-compatible manner. Examples: add output field, add non-mandatory input parameter, use a different tool that produces same results...
- PATCH version (last number): changes/bug fixes that do not affect the api/interface. Examples: typo fix, change/add warning messages...
[ ] All inputs are used in process.
[ ] All output fields have a value assigned to them.

Code that was once accepted should be kept like it is. It should be changed only when its functionality has changed. Small parts may be changed to fix bugs (by changing code only to make it nicer you might introduce a bug).
Set the optimal number of cores that the tool can use (check if parallelization can be performed).
Description of the tool should be self explanatory with links to the tool's homepage and publication.
Write explanatory input labels and add short command line parameter names in square brackets (for example: Maximum length [--maxlength]).
Where possible provide default values for the process input fields. If they are provided, then required = False is not needed.
Add descriptive error and warning messages.
Use Cmd() for each call in the process (call of a tool, a Bash command, a Python script or an R script) and handle return codes.
Add self.progress() calls where appropriate.

Each commit should be minimal (i.e. 1 change) and self-contained (including tests).
Mark incomplete PRs with the [WIP] (Work In Progress) tag.
Do not paste links to private repositories from the public one.

Add meaningful names of test files:
- Genomes: genome_species.fa.gz
- Annotations: annotation_species.gtf.gz
- Adapters: adapters-name/type-source.
Specific files should be saved in a folder with the name of the tested tool. This folder should include separate subfolders for inputs and outputs.
Keep test files' size small. If there is no other option, add the large test file to the files/large directory so it will be tracked with Git LFS.
Pay attention to edge cases: what will happen if any data is missing, if the length of some list is 0, if a string is given where one expects an integer, if a file is empty, ...
When testing workflows, try to verify workflow success by checking one of the last steps. Pick the one that is most likely to fail. Also test that all steps have 'OK' status.