My pipeline update doesn’t seem to do anything

To download new version of a pipeline, you can use the following.

nextflow pull nf-core/<pipeline> -latest

To download a previous version of a pipeline, you can instead use the following, replacing <version> to the corresponding version (v3.4 for example)

nextflow pull nf-core/<pipeline> -r `<version>`

However, in very rare cases, minor fixes to a version will be pushed out without a version number bump. This can confuse Nextflow slightly, as it thinks you already have the ‘broken’ version from your original pipeline download.

This shouldn’t happen with stable versions and normally only happens on dev branches.

If when running the pipeline you don’t see any changes in the fixed version when running it, you can try removing your Nextflow’s nf-core pipeline cache typically stored in your home directory with:

rm -r ~/.nextflow/assets/nf-core/<pipeline>
rm -r ~/.config/nfcore/nf-core/modules

And re-pull the pipeline with the command above. This will install a fresh version of the version with the fixes.