polishing subworkflow - Githubissues

I have added 8 nf-core modules and removed the fastqc module. This updates the modules.json as well.

Next steps:

Clone the polishing branch
Add the local modules, give them both two part names - bed_chunks and bed_coverage for example
```
cp modules/local/bed_chunks/main.nf sanger-tol-genomeassembly/modules/local/bed_chunks.nf
```
Copy the subworkflow - start from the include lines, we don't define nextflow or params within subworkflows.
- I recommend adding some comments so others can take over
- Also extract version information - see example: prepare_genome
Add subworkflow to the workflow
- See example: readmapping
Do linting checks, we have prettier and nf-core lint installed
Do some unit tests, you might need to also update some config files

PR details

[ x] 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).