Implement cram chunking and minimap2-based Hi-C alignments

[reichan1998]

• Adapted hic_bwamem2 and hic_minimap2 from sanger-tol/treeval to chunk HiC CRAM file into containers and align based on read groups.
• Closes Implement minimap2-based Hi-C alignments #97

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
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile 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).

[muffato]

filter_five_end.pl was actually written by the company Arima Genomics. It hasn't been done in TreeVal, but the copyright of this file needs to correctly stated.
Could you please change the copyright statement from being on priyanka (which is false) to:

Copyright (c) 2022-2024 Genome Research Ltd.
except `bin/filter_five_end.pl`:
Copyright (c) 2017 Arima Genomics, Inc.

@tkchafin : if you want to test the feature, try Myxine_glutinosa from TOLSD-2062. We just finished running it with the version 1.2.1 of the pipeline. The resulting CRAM file is 178 GB 🙀 and contains 6.5 billion reads. bwa-mem2 took more than 7 days to run, as a single process on 64 cores and 174 GB RAM.

[tkchafin]

Sent PR reichan1998#2 covering the Illumina case. I think interleaved fastq should be handled correctly there but would be worth a double-check! :)

[tkchafin]

We also need to update the copyright and make sure the documentation is clear on interleaved fastq inputs but will send as a separate PR.
Also need to update CI to run both bwamem and minimap2 tests