Modified on Mon, 19 Sep 2022 at 03:07 AM

Q: Why is Nextflow returning a "... /.git/HEAD.lock: Operation not supported" error?

This problem can occur if your Nextflow pod uses an Azure Files-type (SMB) Persistent Volume as its storage medium. By default, the jgit library used by Nextflow attempts a filesystem link operation which is not supported by Azure Files (SMB).

To avoid this problem, please add the following code snippet in your pipeline's pre-run script field:

cat <<EOT > ~/.gitconfig
    supportsatomicfilecreation = true

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