Missing documentation for ordering of config loading
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Description
Describe the bug
See Slack thread. In short, nf-core pipelines tend to load conf/modules AFTER profiles conf files. This means if you add a custom profile and add it to the list of profiles, you can't change any of the options in conf/modules. The easiest way to get around this is to load a config file (-c) on the command line. This is not very intuitive (in my opinion)
To Reproduce
Steps to reproduce the behavior:
Add a custom profile to the profiles section of a nextflow.config with some options that are also in a conf/modules config. The options in the custom profile will get overwritten.
Expected behavior
A clear and concise description of what you expected to happen.
Ideally, a custom profile will take priority. Minimally, it would be great to add this loading ordering into the documentation.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by locating the website documentation that explains nf-core pipeline configuration and profile loading. Document the ordering of profiles and conf/modules, including the command-line -c workaround, and verify that the resulting guidance explains how custom profiles are affected.
Written by the indexing model from the issue text.
Assessment
- Domain
- documentation
- Issue type
- Documentation
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100