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 #302
• ✨ Add NF-TEST pipeline end-to-end tests for existing CI tests #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 #310
• 🐛 fix params.test_data_base in test and test_full configs #310
• 🤖 GitHub Actions CI - pull_request to dev tests with NXF_VER latest-everything #310
• 🤖 GitHub Actions CI - pull_request to master tests with NXF_VER 22.10.1 & latest-everything #310
• 🤖 GitHub Actions CI - fail-fast set to false #310
• 🐛 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. #322
• 🛠️ rename ignore -> ignore_r1 and ignore_3prime -> ignore_3prime_r1 params
• 🐛 fix ignore_3prime_r2 param #299
• 🐛 removed unused directory #297