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Channel is not one of ['bioconda', 'conda-forge'] #3499

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camlloyd opened this issue Mar 24, 2025 · 0 comments
Open

Channel is not one of ['bioconda', 'conda-forge'] #3499

camlloyd opened this issue Mar 24, 2025 · 0 comments
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@camlloyd
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Description of the bug

nf-core modules lint fails when a wave container is succesfully provisioned, using a channel other than bioconda or conda-forge.

Module in question uses the conda channel ome.

Command used and terminal output

nf-core modules lint bioformats2raw


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

    nf-core/tools version 3.3.0.dev0 - https://nf-co.re


INFO     Linting modules repo: '.'                                                                                                                     
INFO     Linting module: 'bioformats2raw'                                                                                                              

╭─ [!] 2 Module Test Warnings ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                 ╷                                        ╷                                                                                          │
│ Module name     │ File path                              │ Test message                                                                             │
│╶────────────────┼────────────────────────────────────────┼─────────────────────────────────────────────────────────────────────────────────────────╴│
│ bioformats2raw  │ modules/nf-core/bioformats2raw/main.nf │ Unable to connect to container registry, code:  404, url:                                │
│                 │                                        │ https://community.wave.seqera.io/library/bioformats2raw:0.9.4--3eec45888b3759e5          │
│ bioformats2raw  │ modules/nf-core/bioformats2raw/main.nf │ Container versions do not match                                                          │
│                 ╵                                        ╵                                                                                          │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ [✗] 1 Module Test Failed ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                 ╷                                                ╷                                                                                  │
│ Module name     │ File path                                      │ Test message                                                                     │
│╶────────────────┼────────────────────────────────────────────────┼─────────────────────────────────────────────────────────────────────────────────╴│
│ bioformats2raw  │ modules/nf-core/bioformats2raw/environment.yml │ The environment.yml of the module bioformats2raw is not valid: 'ome' is not one  │
│                 │                                                │ of ['bioconda', 'conda-forge']. Check the entry for channels.                    │
│                 ╵                                                ╵                                                                                  │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭───────────────────────╮
│ LINT RESULTS SUMMARY  │
├───────────────────────┤
│ [✔]  35 Tests Passed  │
│ [!]   2 Test Warnings │
│ [✗]   1 Test Failed   │
╰───────────────────────╯

System information

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@camlloyd camlloyd added the bug Something isn't working label Mar 24, 2025
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