Add more nf-tests

[d4straub]

I integrated all test profiles into nf-test tests.

My attempt was the following:
(1) run all tests with nf-test test . --profile=+singularity --update-snapshot --clean-snapshot --verbose
(2) check snapshots, entries that deviated add to one of
(2a) tests/.nftignore (majority of files, when I assumed or experienced that md5sums varied was across several tests)
(2b) tests/.nftignore_files_entirely (file that occurred only sometimes or had variable names, e.g. that contained date/time or database files)
(2c) tests/*.nf.test param ignore: (~line 20) (when I assumed or experienced files with variable md5sums in only one/few tests)
(3) repeat (1) and (2) until there is no change any more

Notable mentions of (2b) are: busco downloads & database hmm & fasta files; ToulligQC output folders contain date & time, as well as NanoPlot log file.

I never checked why those files have unstable md5sums, potentially its worth checking in some cases.
I might have been a little overzealous with not checking file md5sums as in (2a), possible a few more fall into (2c). If there are some specific key files that do not vary (check beforehand!), those could be accommodated.

I think (experienced it, but didnt look more closely, i.e. I might be wrong) that dragonflye assembly is unstable (and therefore all downstream output), as well as Medaka output, but miniasm & Unicycler assemblies are stable. Potentially its worth looking into why and at what point those differ, maybe its possible to change a param or seed to make those results stable.

My plan is to run that tests here also at least 2 times to see if there is any more deviation.

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/bacass 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).

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[d4straub]

Hm I dont get why tests are cancelled without apparent reason. Thats new to me (well, only the 3rd pipeline where I am adding tests...)

Automatically triggered run - shards 5/9 & 9/9 cancelled (but succeeded with latest-everything)
Manually re-triggered shards 5/9 & 9/9 - passed
Manually re-trigger all checks (1) - passed
Manually re-trigger all checks (2) - passed
Manually re-trigger all checks (3) - passed

[Daniel-VM]

Great Job!!! All tests passed. Let me know when this PR is ready for review.

[d4straub]

Thanks. I'll trigger the tests once or twice more to ascertain stable files and file content, but I think its ready for review.

[d4straub]

No failed tests with several triggers, so I think its good to go.

[Daniel-VM]

Awesome. nf-tests integrated perfectly (no tests failed). Well done.

(We will continue improving the stability of the output files generated by Dragonflye and other modules in future versions.)