fix: Cutadapt compression level problem

[uniqueg]

Description

Upgrading Cutadapt resolves the issue (only tested for Conda execution).

Fixes #152

Type of change

Please delete options that are not relevant.

• Bug fix (non-breaking change which fixes an issue)

Conventional Commits guidelines

• I made sure the PR title follows the
  https://www.conventionalcommits.org/en/v1.0.0/

Checklist:

• My code changes follow the style of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing tests pass locally with my changes
• I have updated the project's documentation

[uniqueg]

I didn't change the HTSinfer workflow for which the tests are failing. I assume that is because HTSinfer was updated today and a few other times, recently, probably leading to different results. During heavy development, it was probably okay to always use the latest HTSinfer version - but I think for the publication now we should start pinning the HTSinfer so that we get predictable/reproducible behavior and outcomes (and also support the new HTSinfer Bioconda release).

@balajtimate
@mkatsanto

[balajtimate]

The HTSinfer result JSON was changed in the latest build, so I updated to checksums of the workflow test results to reflect that.

The pipeline was failing with the newest release 0.10.0 of snakefmt (with version 24.1.1 of Black) apparently there was a new line missing from the Snakefile, so added that.

[uniqueg]

Thanks @balajtimate! I am now preparing a PR for #154 - where I will also include the upgrade for Cutadapt. I will leave this open for now, so that we can try out both (in case the other one gives problems).