added classic mlst module

[lskatz]

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. I think I did this right?
• 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:
  • PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd
  • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd
  • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd

[lskatz]

I'm not sure if this is helpful/informative or not

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 2.1



? Lint all modules or a single named module? Named module
? Tool name: mlst
INFO     Linting modules repo: '.'                                                                   __init__.py:157
INFO     Linting module: 'mlst'                                                                      __init__.py:161
╭──────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ Module lint results                                                                                              │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭──────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ [!] 3 Test Warnings                                                                                              │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭──────────────────────────────────────────┬───────────────────────────┬───────────────────────────────────────────╮
│ Module name                              │ File path                 │ Test message                              │
├──────────────────────────────────────────┼───────────────────────────┼───────────────────────────────────────────┤
│ mlst                                     │ modules/mlst/main.nf      │ Could not fetch remote copy, skipping     │
│                                          │                           │ comparison.                               │
│ mlst                                     │ modules/mlst/functions.nf │ Could not fetch remote copy, skipping     │
│                                          │                           │ comparison.                               │
│ mlst                                     │ modules/mlst/meta.yml     │ Could not fetch remote copy, skipping     │
│                                          │                           │ comparison.                               │
╰──────────────────────────────────────────┴───────────────────────────┴───────────────────────────────────────────╯
╭───────────────────────╮
│ LINT RESULTS SUMMARY  │
├───────────────────────┤
│ [✔]  22 Tests Passed  │
│ [!]   3 Test Warnings │
│ [✗]   0 Test Failed   │
╰───────────────────────╯

[drpatelh]

Looks great @lskatz ! Mainly minor changes as a result of recent updates we are trying to push to nf-core/modules. Sorry, a little bit of bad timing here.

The CI tests will be stalled because have maxed them out updating all of the other modules #739. In any case, I think it would be a good idea to get that PR in first and then we can come back to get this in after you have made the appropriate changes :)

[lskatz]

Thank you! I made changes locally so that I could get the muscle memory and pushed those changes to this PR.

[rpetit3]

@drpatelh I think we are good here, as long as @lskatz agrees with my switch to > ${prefix}.tsv for the result output.

[drpatelh]

Thanks guys!