DSL1: Release 2.5.0 - Bopfingen

[TCLamnidis]

Better RG information generated by all mappers. Bumped MultiQC. Faster processing, and always produces general_stats_table.txt. MapDamage2 can now be used for damage calculation. Read number limit available for large input files. Fixed a bug where genotyping and damage calculation would not run if using bowtie2 and no fasta index was provided.

PR checklist

• [x] This comment contains a description of changes (with reason).
• [x] If you've fixed a bug or added code that should be tested, add tests!
  • [ ] If you've added a new tool - add to the software_versions process and a regex to scrape_software_versions.py
  • [ ] 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/eager branch on the nf-core/test-datasets repository.
• [x] Make sure your code lints (nf-core lint .).
• [x] Ensure the test suite passes (nextflow run . -profile test,docker).
• [x] Usage Documentation in docs/usage.md is updated.
• [x] Output Documentation in docs/output.md is updated.
• [x] CHANGELOG.md is updated.
• [ ] README.md is updated (including new tool citations and authors/contributors).

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