srst2/srst2 to nf-test

[famosab]

PR checklist

Closes #7700

• 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

[SPPearce]

Looks like meta.db should probably be a value channel.
The pileup file seems to be unstable too.

[famosab]

│ htsjdk.samtools.SAMException: Sequence name '347__lmr(B)__lmr(B)__00005' doesn't match regex: '[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*'                                                                                   │
│ htsjdk.samtools.SAMException: Sequence name '347__lmr(B)__lmr(B)__00005' doesn't match regex: '[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*'  

[famosab]

@jvhagey Do you think we can remove the bacteroides fragilis test? Becaus ethat one seems to cause the samtools errors.

[SPPearce]

@jvhagey Do you think we can remove the bacteroides fragilis test? Becaus ethat one seems to cause the samtools errors.

I'd say just remove it if we can't figure it out, yes.

[famosab]

I decided to comment the tests out for now. There are a couple of instabel things even with the working test data. But for the sake of getting this finished up I would vote for merging this soon. And if the module ever gets updated (unlikely as the tool has not been changed since 2016) this can be tackeld again!