Template merge 3.3.1

[jonasscheid]

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/mhcquant 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).

[marissaDubbelaar]

Two minor questions, also why are the tests not running through?
Can we ignore that for this PR?

[marissaDubbelaar]

Can this parameter be removed?

[jonasscheid]

I still did not fully understand what happened, but if I don't remove the optional mzml filter, there are no spectra anymore and the pipeline resulted in having no actual results, just intermediate.

[marissaDubbelaar]

That sounds very dubious I must say 😅.
If the test can be ignored for now, then I can approve it from my side (if you still need approval at least)

[jonasscheid]

I think so.. See #379 (comment)
@marissaDubbelaar PR is ready to review :)

[jonasscheid]

There is some floating point rounding error going on that let nf-test fail.
e.g.
Column 16:
LEFT: 98.16315917968744
RIGHT: 98.16303710937495
Column 18:
LEFT: 1149.8631591796875
RIGHT: 1149.863037109375
Column 20:
LEFT: 98.16315917968744
RIGHT: 98.16303710937495

I'll adjust the test such that it checks for content

[jonasscheid]

@maxulysse do you know the plan for test_fullprofile? Is there a snapshot needed (for AWS tests on-release)?

[maxulysse]

@maxulysse do you know the plan for test_fullprofile? Is there a snapshot needed (for AWS tests on-release)?

We only test that it launches and finish without failures.