Snapshot for -profile test_assembly_input

[dialvarezs]

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/mag branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[dialvarezs]

@nf-core-bot fix linting

[dialvarezs]

Ok, after a long time struggling this the stability of this snapshot, it's finally ready for merging.

The instability because of:

• An issue of the publishing of BUSCO files, it's fixed now
• Inconsistent sorting on CSV files. I added a sort step in the Python scripts to keep bin_summary.tsv stable.

Regarding BUSCO, I found out that is not able to produce consistently sorted CSV batch files, even when running with a single core... So I decided to left out of the snapshots both *.batch_summary.txt and busco_summary.tsv.

[dialvarezs]

I also updated the get_mag_depths.py script to produce depth summaries with consistent column ordering, to prevent swapped depth values on the merged depth summary.

[d4straub]

I got a few questions, but generally I think the PR is great, and it uncovered already some bugs, thats what its for! :)

[dialvarezs]

I added some basic CSV checks for busco_summary and bin_summary files. I also updated the nft-utils plugin.
And fixed the error reporting of tiara_classify that was breaking the test_alternatives test.

Most of the small fixes I did on this PR originally were ported to other PR for v5.2.0, so this PR has become more simple now.

[prototaxites]

A few questions/comments, but this is looking fine as-is!