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

[human9]

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.

[awgymer]

The culprit is

tools/nf_core/create.py

Line 172 in 930ece5

param_dict["name"].lower().replace(r"/\s+/", "-").replace(f"{param_dict['prefix']}/", "").replace("/", "-")

It is converting the 'name' (which at this point contains the prefix, because it is pulled from manifest.name) to lowercase before it tries to replace the prefix value with an empty string.

We have two options:

• convert name to lowercase after replacing prefix
• ensure prefix is only ever lowercase on initial creation

[human9]

Nice, I guess it's a matter of deciding whether the bug is that name gets mangled, or that an uppercase prefix is allowed at all. My 2 cents is that taking the first option is the less disruptive option, as although it might have been intended otherwise uppercase prefixes are currently allowed.