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GitHub Authentication fails silently #5906

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tobsecret opened this issue Mar 20, 2025 · 0 comments
Open

GitHub Authentication fails silently #5906

tobsecret opened this issue Mar 20, 2025 · 0 comments

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@tobsecret
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tobsecret commented Mar 20, 2025

Bug report

Expected behavior and actual behavior

Expected behavior:
When trying to authenticate with GitHub (or other services) and failing, Nextflow should give a clear warning, then continue to try and perform what it tried unauthenticated.

Observed behavior:
Nextflow GitHub authentication fails silently, then tries to pull from GitHub unauthenticated. This sometimes works and sometimes hits the GitHub unauthenticated rate limit. Because we don't get a warning that our authentication failed, it's not clear if our token reached the rate limit or if authentication failed.

Steps to reproduce the problem

nextflow.config

providers {
    github {
        user = 'myuser'
        password = 'a_token_mistakenly_used_as_a_password'
    }
}

pull_repo.sh

nextflow pull nf-core/sarek

Program output

Pulling nf-core/sarek ...
WARN: Cannot read project manifest -- Cause: API rate limit exceeded -- Provide your GitHub user name and password to get a higher rate limit
API rate limit exceeded -- Provide your GitHub user name and password to get a higher rate limit

Sometimes this will work despite no authentication since GitHub does allow some amount of unauthenticated requests per hour.

Environment

  • Nextflow version: 24.10.5
  • Java version: [?]
  • Operating system: linux
  • Bash version:

Additional context

Ran into this in our build and testing pipeline which was both using outdated credentials and an incorrect config file. I thought that the problem was using password instead of token but a message telling me that Github Authentication failed would have been helpful. If this is available via verbose nextflow, I think this should be printed by default even without verbose.

UPDATE: still failing, even when using token instead of password

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