`nf-core sync` will modify the template incorrectly if the pipeline prefix is uppercase

Description of the bug

nf-core sync seems to parse the workflow name incorrectly (?) if the prefix is uppercase, causing problems updating the template.

Steps to reproduce

• Create a blank pipeline using nf-core create, and provide an uppercase prefix when prompted
  • e.g. create a pipeline called UPPER/pipeline
• The created template should look normal, under workflows there should be pipeline.nf.
• Run nf-core sync from the main branch (or dev)

Result

In the TEMPLATE branch, most instances of the workflow name "pipeline" have been renamed to "upper-pipeline". e.g. pipeline.nf is renamed to upper-pipeline.nf.

This doesn't happen when a lowercase prefix is provided instead, i.e. a pipeline called upper/pipeline will not reproduce this.

Command used and terminal output

# no commands actually fail

System information

• nextflow 24.03.0-edge
• nf-core: 2.14.1
• Python 3.12.3
• Ubuntu 24.04

Extra edit

I had created a pipeline with upper case prefix, and broke it by syncing as described.
There are only two changes I needed to commit to fix it:

• change to lowercase prefix in .nf-core.yml
• fix the workflow name in nextflow.config (under manifest).

The next nf-core sync then works as expected.

Reproduce the issue by creating an uppercase-prefix pipeline, then run nf-core sync and compare pipeline.nf, .nf-core.yml, and nextflow.config with the generated TEMPLATE branch. Trace the nf-core sync entry point and identify where the prefix is parsed; done means uppercase prefixes preserve the workflow name and the synced template remains consistent.