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
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    • nf-core modules test <MODULE> --profile docker
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    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
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[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

[dialvarezs]

Hi Jim,

Supporting gzipped input is a nice adittion to have. And thank you for looking into the issues when running Prokka, because sometimes becomes mysteriously unreliable for some reason.

Aside from the minor changes I proposed, if you have time, can you please add the stub and the stub test?

Thank you.

[prototaxites]

Added stub & corresponding test.

If anyone knows how to convert the oras:// identifier to https://, please let me know!

[dialvarezs]

Great, it's ready to merge then!