dsl2: metagenomics uncollapsed paired end

[ilight1542]

Draft PR for metagenomics paired-end merging off.

This is a QOL improvement for tools that can use paired end information (kraken2, krakenuniq), and now allows for variable inputs into these tools (by splitting inputs into either PE or SE data and running separate instances).

Main issues resolved:

• input parsing for paired-end compatible tools (kraken2, krakenuniq, metaphlan) added when --preprocessing_skippairmerging used.
• Mixed paired end/single end data parses OK and outputs are properly saved
• Warning for users that singletons are not assessed when skipping pairmerging. and metaphlan, which does not use paired end information should likely not be used with this parameter.

TODOs:

• for metagenomics generally - check that behavior of mapped/all is distinct, ensure that samtools.fastq.out.other is distinct for these two modes
• possibly merge all reads back to a single file for --metagenomic_input all

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 - 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](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
  • If necessary, also make a PR on the nf-core/eager 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).
• 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).