Add clustalo as aligner to fasta_newick_epang_gappa swf

[erikrikarddaniel]

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

This adds clustalo, in profile mode, as aligner to the subworkflow in addition to hmmalign and mafft.

[SPPearce]

Haven't looked properly, but can you not use it implicitly in the map/filter's - the new language server will warn about that.

[erikrikarddaniel]

Haven't looked properly, but can you not use it implicitly in the map/filter's - the new language server will warn about that.

That should be done now.

[SPPearce]

I think that the tests could be combined into one single snapshot, rather than lots of individual ones, but that isn't essential.

[erikrikarddaniel]

I think that the tests could be combined into one single snapshot, rather than lots of individual ones, but that isn't essential.

That would indeed have fixed my typos -- thanks for finding them.

There are three reasons why the tests look like they do. First is maybe rather lame: I'm still learning nf-test and just don't know what I can do yet. Second, is what I think is a showstopper: Some of the outputs can't be snapshot since there are timestamps and other things in the output files (this includes the two files you found I had typos in). Third is my general preference for granular tests and thinking that individual tests make it easier to spot what broke. Maybe this is partly because of my lack of complete understanding of nf-test though.

[SPPearce]

Ok, that's fine

[erikrikarddaniel]

Thanks!