Changes:
 - Moves every local module into a named subfolder
 - Each module uses a main.nf file
 - Improves consistency between modules (local and nf-core)
 - Should make it easier to create nf-tests

Fixes #1080

- [ ] 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](https://github.com/nf-core/rnaseq/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/rnaseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
- [ ] Make sure your code lints (`nf-core lint`).
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir \u003cOUTDIR\u003e`).
- [ ] 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).

 - Moves every local subworkflow into a named subfolder
 - Each workflow uses a main.nf file
 - Improves consistency between subworkflows (local and nf-core)
 - Should make it easier to create nf-tests