add ctatsplicing/prepgenomelib and ctatsplicing/startocancerintrons

[anoronh4]

PR checklist

Closes rnafusion#628

The reason I am only doing stub tests only is for practicality. The smallest reference i could get was about half a Gb, even when starting with the minigenome.fa and minigenome.gtf suggested by the tool's maintainers. I also considered adding starfusion/build so that i wouldn't have to store the reference on test-datasets, however this takes almost an hour to run on my system.

• 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]

Great job on migrating these modules to nf-core modules! Left a few suggestions for small details. I am also tagging the author of these local modules, @nvnieuwk , so that he can give a final look in case I am missing something. There is an open PR here: #8107 which is adding the STARFUSION process, which could come very useful to add the non-stub test.

[nvnieuwk]

The main reason I couldn't add these modules to the nf-core/modules repository is because of the containers. These are third party containers so we don't really have any control over what happens with these... I think it would be worth it to either look into adding these modules to bioconda first or at least add these containers to the nf-core quay repo if bioconda isn't an option

[anoronh4]

i'm guessing bioconda is an option because i see other ctat packages have recipes there. i have never done this before but am willing to give it a shot.