Add nf-core module and subworkflow mirdeep2

[atrigila]

This PR adds modules and a subworkflow associated with mirdeep2.

Part of the migration from local to nf-core modules in nf-core/smrnaseq#368 to match latest standards and improve quality.

Closes nf-core/smrnaseq#431

PR checklist

Closes #XXX

• 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 module conventions in the contribution docs
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Emit the versions.yml file.
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[atrigila]

There is an issue with java.nio.channels.OverlappingFileLockException #6664 in the conda subworkflow test

[atrigila]

The conda issue persists but, I will fix the new linting issues with the dev version of nf-core tools and nf-core modules lint --fix

[atrigila]

Thank you @sateeshperi!