Dev -> Master 2.4.0

[sateeshperi]

Pipeline Updates

• Updated template to nf-core/tools v2.8
• Add --bamqc_regions_file parameter for targeted methylation sequencing data Regions file parameter for Qualimap Bamqc #302
• ✨ Add NF-TEST pipeline end-to-end tests for existing CI tests bump-nf-tests-snapshots-2.8.0 #310
• NF-TEST pipeline Assertions - ✨ Featuring NF-TEST Snapshots, new File().exists() and !new File().exists() checks
• 🛠️ tests/pipeline/UTILS.groovy for local groovy functions used in tests

Bug fixes & refactoring

• 🛠️ update index file channels to explicit value channels bump-nf-tests-snapshots-2.8.0 #310
• 🐛 fix params.test_data_base in test and test_full configs bump-nf-tests-snapshots-2.8.0 #310
• 🤖 GitHub Actions CI - pull_request to dev tests with NXF_VER latest-everything bump-nf-tests-snapshots-2.8.0 #310
• 🤖 GitHub Actions CI - pull_request to master tests with NXF_VER 22.10.1 & latest-everything bump-nf-tests-snapshots-2.8.0 #310
• 🤖 GitHub Actions CI - fail-fast set to false bump-nf-tests-snapshots-2.8.0 #310
• 🐛 get to the bottom of index tests Get to the bottom of index tests #278
• ✨ Support for Bismark methylation extraction ignore and ignore_3prime parameters when ignore_r1 or ignore_3prime_r1 are greater than 0. 2.4.0 code review fixes #322
• 🛠️ rename ignore -> ignore_r1 and ignore_3prime -> ignore_3prime_r1 params
• 🐛 fix ignore_3prime_r2 param --ignore_r2 and --ignore_3prime_R2 are not working as intended #299
• 🐛 removed unused directory stranded_CpG_report folder is empty #297

[SPPearce]

I don't think that ignore is a suitable name for a parameter, I think it should be ignore_r1. Similarly with ignore_3prime to make it match up.
Generally ok other than that, a few minor points. There are some #TODO strings, I don't know if that is because they are in the template or where they have come from.

[SPPearce]

Can you check the genome question, otherwise should be good to go.

[edmundmiller]

Looks good to me! Only thing is copilot may have eaten the <int> calls.