Cp updates

[mahesh-panchal]

Changes

• Use path objects for path strings
• Use resolve() to correctly get filenames for cross platform-portability.
• Removes null channel injections
• Trim workflow of combine -> multiMap patterns.
• Add test for crai existance
• Strip , from RG headers (DS field) which caused errors with DTOL archived reads.

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
• If necessary, also make a PR on the sanger-tol/curationpretext 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 --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).