Final changes for milestone 2.2.0

[charles-plessy]

This PR brings the last round of changes that I would like to see in version 2.2.0:

• Allow skipping assembly QC,
• Allow export to more than one format at a time,
• Combine redundant containers,
• Fix tube map,
• Bump version to 2.2.0.

I plant to request the merge from dev to master after this PR is done, and keep the upcoming 3.3.0 template update for a 2.2.1 minor update, to simplify review.

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/pairgenomealign 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).

[Felix-Kummer]

For me, who was no bioinformatics background, this is a bit confusing.
It is unclear what these .maf files are (inputs or outputs).
Adding module names may also improve the alignment with the short pipeline description in the readme file.
Not a blocker though as this is likely caused by my limited knowledge on bioinformatics.

[Felix-Kummer]

Just a minor comment on the tubemap, but not a blocker.

[charles-plessy]

@Felix-Kummer Thank you! Point taken in #74 and #75.