Update Prokka to take compressed input && tidy module script

[prototaxites]

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

[prototaxites]

Undoing container build bump - there's some kind of java version error with minced that I'm getting when running with Singularity on our HPC (but not on Gitpod).

See tseemann/prokka#557 for details - bumped container image has a version of java that's too new:

Original image:

╰λ singularity shell $NXF_SINGULARITY_CACHEDIR/depot.galaxyproject.org-singularity-prokka-1.14.6--pl5321hdfd78af_4.img 
Singularity> java --version
openjdk 11.0.9.1-internal 2020-11-04
OpenJDK Runtime Environment (build 11.0.9.1-internal+0-adhoc..src)
OpenJDK 64-Bit Server VM (build 11.0.9.1-internal+0-adhoc..src, mixed mode)
Singularity> exit

Bumped image:

╰λ singularity shell $NXF_SINGULARITY_CACHEDIR/depot.galaxyproject.org-singularity-prokka-1.14.6--pl5321hdfd78af_5.img 
Singularity> java --version
openjdk 20.0.2-internal 2023-07-18
OpenJDK Runtime Environment (build 20.0.2-internal-adhoc..src)
OpenJDK 64-Bit Server VM (build 20.0.2-internal-adhoc..src, mixed mode, sharing)

[prototaxites]

The minced binary is built with Java version 8 - I've switched the container to a Sequera container with the correct OpenJDK version pinned, and updated the Conda environment to match.

Testing seems to have fixed the problem on our cluster; hopefully will fix this intermittently reported issue in mag too: nf-core/mag#552