A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

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Which command on what type of repository did you run?

`master` is the old name of the default branch in git repositories, but this term is reminiscent of slavery, so the tech industry and also nf-core decided to rename the default branch. While `primary` is at times also used, `main` emerged as the most common alternative and is also used on nf-core repos now.

So it should be looking for a `main` branch instead. It may be as simple as renaming the default branch on your local repository as well, but a bit more context would help to be sure.

```git branch -m master main```

Wait a sec…on the modules repo, it seems the branch name is still master?

Yes, I was in the modules repo, the command wa following `nf-core modules lint gapseq/findtransport`

Does the error persist? GitHub had issues this week and the `master` branch should actually exist. So maybe it was just an outage that has resolved?

I've checked one more time and I still have this error

I executed the same command during the week and everything was fine and today it is always this hiccup

In a different folder: Does `git clone git@github.com:nf-core/modules.git` work normally?

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You should check that your key <https://docs.github.com/en/authentication/troubleshooting-ssh/error-permission-denied-publickey#make-sure-you-have-a-key-that-is-being-used|is used correctly> and that <https://docs.github.com/en/authentication/troubleshooting-ssh/error-permission-denied-publickey#verify-the-public-key-is-attached-to-your-account|you have it set up>.

The problem is usual a faulty module cache. Can you try to remove  `~/.config/nfcore/nf-core/modules`

^ this has saved me more than once since you taught me only last week :sweat_smile:

Sorry Olga for the suggestions that led you totally astray. :smiling_face_with_tear:

&gt; The problem is usual a faulty module cache.
If that is a such a common problem that it has saved Pieter more than once during a single week, I wonder if we could fix that by preemptively refreshing the modules cache if <#CE5LG7WMB>  hits a Git error?

This <https://github.com/nf-core/tools/blob/b6c5737fde996c824b87d19d1c51a29b4810db1d/nf_core/pipelines/download/workflow_repo.py#L261-L263|is the standard behavior> for `nf-core pipelines download` ’s cached WorkflowRepo class since its introduction and as far as I can tell this silent error recovery mechanism has worked quite well so far.

I might just be more trigger happy when it comes to git rebasing than other folks though :wink: I think that's what caused most of my issues. Although I suspect it also popped up once after a pipeline sync or modules update.

I was not alone with the error -  that matters the most