New module structure breaks patch file functionality

[adamrtalbot]

Description of the bug

After the recent update to the new module structure in https://github.com/nf-core/modules, all nf-core modules operations. When using the latest version of nf-core tools (dev, 2.6) many errors are occurring which are being solved as part of #1867

However! diff files created by previous versions of nf-core module patch still cause problems. The existing paths create issues for the tools:

nf-core modules update --all -y
...
FileNotFoundError: [Errno 2] No such file or directory: 'modules/nf-core/modules/bcftools/filter/bcftools-filter.diff'

To recreate this problem, clone the repo: https://github.com/adamrtalbot/rnaseq/tree/nf-core_2.6_update_problems and run nf-core modules update. This repo has had a patch applied to the tar module with v2.5.1 and is then updated to 2.6 afterwards.

To fix:

• The path must be corrected in the modules.json
• The paths within the .diff file itself must be corrected

Once this is done nf-core modules functionality works.

This does not seem to affect patches performed after updating to 2.6.

Command used and terminal output

nf-core modules update

# On repo: https://github.com/adamrtalbot/rnaseq/tree/nf-core_2.6_update_problems

System information

No response