Release v1.1.0 that adds a new softmask parameter, to optionally keep original softmasking.

[charles-plessy]

I have added a new softmask parameter, with default value of tantan that keeps the 1.0.0 pipeline behaviour. When set to original the new parameter causes the pipeline to keep the original soft-masking of the target genome instead of overriding it with tantan. No other values are accepted thanks to the nextflow schema. The patch on the schema is a bit heavy because I also grouped the seed and the softmask parameter in a new group of options.

There are no lint errors and I will wait for after the next nf-core tools release to address the update warnings.

By the way I need a Zenodo DOI for the pipeline and I was told on Slack that the core team needs a new release for this to happen.

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 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).

[ewels]

Needs to go to dev first. Then a PR from dev to master for release.

See the release checklist: https://nf-co.re/docs/checklists/pipeline_release