add crabs/dbimport from readsimulator pipeline and rename to crabs/import

[famosab]

PR checklist

Closes #5532

• 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

[famosab]

CRABS has changed a lot of its functionality when updating to version 1.0.0. This needs to be taken care of!

[famosab]

Seems like the versions.yml is different for the conda package (there null is returned as version which is obviously wrong). But when I test it locally it works fine and returns the version as expected.

[famosab]

nf-core modules test crabs/dbimport --profile conda                                                                                                                                                  [12:58PM]


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

    nf-core/tools version 3.2.0 - https://nf-co.re


INFO     Generating nf-test snapshot                                                                                                                                                                                                                                                             
╭─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── nf-test output ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                                                                                                                                                                                                                                                                                               │
│ 🚀 nf-test 0.9.2                                                                                                                                                                                                                                                                              │
│ https://www.nf-test.com                                                                                                                                                                                                                                                                       │
│ (c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr                                                                                                                                                                                                                                          │
│                                                                                                                                                                                                                                                                                               │
│ Load .nf-test/plugins/nft-bam/0.5.0/nft-bam-0.5.0.jar                                                                                                                                                                                                                                         │
│ Load .nf-test/plugins/nft-compress/0.1.0/nft-compress-0.1.0.jar                                                                                                                                                                                                                               │
│ Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar                                                                                                                                                                                                                                         │
│ Load .nf-test/plugins/nft-csv/0.1.0/nft-csv-0.1.0.jar                                                                                                                                                                                                                                         │
│ Warning: every snapshot that fails during this test run is re-record.                                                                                                                                                                                                                         │
│                                                                                                                                                                                                                                                                                               │
│ Test Process CRABS_DBIMPORT                                                                                                                                                                                                                                                                   │
│                                                                                                                                                                                                                                                                                               │
│   Test [c8d9c787] 'sarscov2 - fasta' PASSED (50.227s)                                                                                                                                                                                                                                         │
│   Test [97fec540] 'sarscov2 - fasta - stub' PASSED (35.526s)                                                                                                                                                                                                                                  │
│                                                                                                                                                                                                                                                                                               │
│                                                                                                                                                                                                                                                                                               │
│ SUCCESS: Executed 2 tests in 85.766s                                                                                                                                                                                                                                                          │
│                                                                                                                                                                                                                                                                                               │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
INFO     Generating nf-test snapshot again to check stability                                                                                                                                                                                                                                    
╭─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── nf-test output ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                                                                                                                                                                                                                                                                                               │
│ 🚀 nf-test 0.9.2                                                                                                                                                                                                                                                                              │
│ https://www.nf-test.com                                                                                                                                                                                                                                                                       │
│ (c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr                                                                                                                                                                                                                                          │
│                                                                                                                                                                                                                                                                                               │
│ Load .nf-test/plugins/nft-bam/0.5.0/nft-bam-0.5.0.jar                                                                                                                                                                                                                                         │
│ Load .nf-test/plugins/nft-compress/0.1.0/nft-compress-0.1.0.jar                                                                                                                                                                                                                               │
│ Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar                                                                                                                                                                                                                                         │
│ Load .nf-test/plugins/nft-csv/0.1.0/nft-csv-0.1.0.jar                                                                                                                                                                                                                                         │
│                                                                                                                                                                                                                                                                                               │
│ Test Process CRABS_DBIMPORT                                                                                                                                                                                                                                                                   │
│                                                                                                                                                                                                                                                                                               │
│   Test [c8d9c787] 'sarscov2 - fasta' PASSED (37.762s)                                                                                                                                                                                                                                         │
│   Test [97fec540] 'sarscov2 - fasta - stub' PASSED (36.477s)                                                                                                                                                                                                                                  │
│                                                                                                                                                                                                                                                                                               │
│                                                                                                                                                                                                                                                                                               │
│ SUCCESS: Executed 2 tests in 78.64s                                                                                                                                                                                                                                                           │
│                                                                                                                                                                                                                                                                                               │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
INFO     All tests passed!   

It works locally with exactly the snapshot that is part of this PR, I do not understand why accessing the version does not work in the CI.

This works on my Mac as well as on our linux workstation...

[famosab]

@fellen31 The problem seems to persist. Locally I get the version as shown in my terminal output but in the CI the version is reported as null.