How to get nextflow pull to work with github enterprise

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1

I want to be able to run:

nextflow pull https://github.com/AI-Digital-Research/targetevaluator

which is a private repo in github enterprise

I normally access the github with ssh keys, I dont think there is the option to create an access token.

What bash vars do I need and how do I set up the scm file?

Thanks in advance

2

Hey, @Sam_Neaves. You will find instructions on configuring your credentials to pull private repositories here, in the official docs.

It’s basically adding credentials about the SCM provider in the $HOME/.nextflow/scm file, like:

providers {
    github {
        user = 'your-user-name'
        password = 'your-personal-access-token'
    }
}

Pay attention to the green box with instructions for the GitHub token in recent versions of Nextflow :wink:

3

Thanks for the reply. I found that information but still no luck in getting it to work :S

I get an error:

WARN: Cannot read project manifest – Cause: Remote resource not found:

4

Please check the discussion here and see if you can make it work by using what Trevor did. Then, let me know of the outcome, please :slight_smile:

5

Hey, @Sam_Neaves. Have you managed to make it work? :slight_smile:

6

Thanks for the reply and follow up. I have been taken off working on this for the time being so I have not tried your suggestions.

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