nf-core v2.14 update

[tkchafin]

Solves #70

(1) nf-core v2.13 migration:

• Removal of lib/ directory in favour of new boilerplate sub workflows
• Switch to nf_validation for sample sheet checking + removal of local module for sample sheet checking -> validated sample sheet is now passed directly to input_check.nf sub workflow, which just runs SAMTOOLS_FLAGSTAT and formats channels for alignment sub workflows.
• Moved start-up and completion steps to new sub workflows PIPELINE_INITIALISATION and PIPELINE_COMPLETION defined in subworkflows/local/utils_nfcore_readmapping_pipeline

(2) nf-core v2.14 migration

• A number of changes proposed to the .github/workflows were rejected, with exception of: (a) added new download_pipelines.yml; (b) update nf-core setup version in ci.yml
• Minor changes to a number of config files
• Full template update (pushed to TEMPLATE branch Template update for nf-core/tools version 2.14.1 #98)

(3) Other

• nf-core modules and sub workflow updates
• Update Samtools v1.17 -> v1.20 in local modules

NOTES:

1. The INPUT_CHECK sub workflow now only has a single module step, so could probably be removed and just call the module directly in readmapping.nf
2. There is a redundant "monochromeLogs" parameter in nextflow.config... This is needed by nf-validation. This is fixed in nf-schema, however nf-schema can't be used alongside nf-validation, which is still required by subworkflows/nf-core/utils_nfvalidation_plugin so for now I stick to nf-validation:1.13

PR checklist

• This comment contains a description of changes (with reason).
• 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).

[tkchafin]

Still need to fix linting issues, not ready for review

[tkchafin]

ready for review

[BethYates]

I'm not sure if this is intended or not but when you run the pipeline using the test profile it now asks for an --outdir param because the default value in modules.config has changed from "./results" to null. This makes sense as the docs say this is a required parameter but do we want to maybe set a default value for --outdir in the test and test_full profiles?