Pull request for release of 2.1.0

[jfy133]

This PR is for the nf-core/eager release 2.1.0 (Ravensburg).

Please see the CHANGELOG.md for a complete list of changes.

This release includes extensive changes to the channel logical, allowing a user to turn on/off modules (i.e. skipping processes).

This release makes nf-core/eager reach essentially functional parity with EAGER 1 with:

• Genotyping: GATK HaplotypeCaller, GATK UnifiedGenotyper (and bonus addition of FeeBayes)
• Endogenous DNA calculation: endorS.py
• Mitochondrial to Nuclear Ratio: MT2NucRatio

It also includes additional functionality, specifically in allowing automated metagenomic screening typically used in ancient pathogen and microbiome work

• Taxonomic binning: MALT, Kraken
• High-throughput aDNA screening: MaltExtract
• SNP Table generation: MultiVCFAnalyzer
• Feature statistics (e.g. gene depth/breadth): bedtools

Additional functionality:

• Human nuclear contamination estimation
• Human sex determination

Finally, it comes with a extensive usage and output documentation with useful schematic diagrams and a great new logo.

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 necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repo
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Make sure your code lints (nf-core lint .).
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated

Learn more about contributing: https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md

[apeltzer]

Can't find anything, but I reviewed this like 10x already in all the individual steps :-/

[maxibor]

Finished review. Overall, my main suggestion is to remove the hardcoded default values in the help menu of eager, and replace them with ${params.parameter}.
This is because the defaults might change depending on the configuration file used.