Kallisto module

[opetryk]

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/lncpipe 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).

What this pull request contains:

1. new module downloaded from nf-core modules - kallistio/index and kallistio/quant in modules/nf-core/ directory
2. Kallistio quant requires few additional parameters that were added to nextflow.config and schema file (used nf-core tools for additing parameters into schema)

What should be done:

1. integraton of the tool into the workflow
2. provide default values for kallistio_fragment_length and kallistio_fragment_length_sd
3. parameters like kallisto gtf and kallisto_chromosomes are optional parameters and can be handed in a way:

ch_kallisto gtf = params.kallisto gtf ? Channel.fromPath(params.kallisto gtf , checkIfExists: true) : []
4. documentation (?)

[Emeerdink]

Seems good. Kallisto now needs to be added to the lncpipe.nf file. I would like to do this in the same PR if possible. Keep it open until I figure this out.