Update nf-tests and language server fixes

[LouisLeNezet]

• Fix image in usage.md.
• Fix small warnings and errors with updated language server.
• def has been added when necesary, `
• :use instead of,` in assertions,
• _ added to variables not used in closures,
• for loop replaced by .each{},
• remove unused code / input.
• Fix getFileExtension function.

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/phaseimpute 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).

[atrigila]

• Small suggestions to document the reason for the changes in the PR.
• Add information to changelog.
• Test (and post results) of the full chromosome test before the full test.

[atrigila]

Thanks for the PR. There’s a lot of great work in here. I noticed, though, that the scope of this PR is still a bit broad. Since the main focus is on "reducing computational time for the AWS megatest," could we keep this PR to just those specific changes? Some of the updates seem unrelated, and reviewing all 64 files at once makes it a bit tough to keep things focused.

Would you mind splitting out the unrelated changes into separate PRs (e.g. subworkflow snapshots, major language server fixes)? I'll make it better for me to give each code the attention it deserves. Also, include the results of at least one full chromosome test (you can run it on a large gitpod instance with a small sample and it shouldn't take that long) showing the performance improvement will be super helpful to speed up the review.

[LouisLeNezet]

The scope of the PR has been changed to only fix the language server and nf-test updates.
The fulltest changes has been moved to #158