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'nf-core modules list local --json' reports empty list #2665

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adamrtalbot opened this issue Jan 17, 2024 · 1 comment
Closed

'nf-core modules list local --json' reports empty list #2665

adamrtalbot opened this issue Jan 17, 2024 · 1 comment
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@adamrtalbot
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adamrtalbot commented Jan 17, 2024

Description of the bug

If we use nf-core modules list local we get a nice output of all modules. If we use nf-core modules list local --json we get a blank list. Example from fetchngs but it also happens on rnaseq.

Command used and terminal output

> nf-core modules list local

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

    nf-core/tools version 2.11.1 - https://nf-co.re


INFO     Modules installed in '.':                                                                                                                                                                                     
                                                                                                                                                                                                                       
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━┓
┃ Module Name                 ┃ Repository                             ┃ Version SHA                              ┃ Message                                               ┃ Date       ┃
┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━┩
│ custom/sratoolsncbisettings │ https://github.com/nf-core/modules.git │ 20e78a9868eaa69c8cac91152397def32374b807 │ Replace base path for test data with new form (#4723) │ 2024-01-12 │
│ sratools/fasterqdump        │ https://github.com/nf-core/modules.git │ 20e78a9868eaa69c8cac91152397def32374b807 │ Replace base path for test data with new form (#4723) │ 2024-01-12 │
│ sratools/prefetch           │ https://github.com/nf-core/modules.git │ 20e78a9868eaa69c8cac91152397def32374b807 │ Replace base path for test data with new form (#4723) │ 2024-01-12 │
│ untar                       │ https://github.com/nf-core/modules.git │ 20e78a9868eaa69c8cac91152397def32374b807 │ Replace base path for test data with new form (#4723) │ 2024-01-12 │
└─────────────────────────────┴────────────────────────────────────────┴──────────────────────────────────────────┴───────────────────────────────────────────────────────┴────────────┘


> nf-core modules list local --json

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

    nf-core/tools version 2.11.1 - https://nf-co.re


[]

System information

nf-core, version 2.11.1

@mashehu
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mashehu commented Feb 9, 2024

fixed in #2668

@mashehu mashehu closed this as completed Feb 9, 2024
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