Include config `modules.config` in the wrong place ?
A pull request for this has already been merged.
- #3301 by @LouisLeNezet — merged
- Dominant language
- Python
- Stars
- 322
- Forks
- 255
- Avg merge
- 2d 3h
- Merged PRs (30d)
- 5
Description
Description of the bug
Hi !
With the new version of the template the import of the modules.config files as been moved to the bottom of the nextflow.config file.
However all the test config files are imported above in the nextflow.config and therefore any modification to a process present in both a test.config and in the modules.config would be overwritten by the later.
This does happen in phaseimpute and we just moved it next to base.config.
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
What were the rational for this modification ?
Command used and terminal output
System information
No response
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Research direction
Review the template’s nextflow.config alongside conf/base.config, conf/modules.config, and the test config files to verify the include order and the reported override in phaseimpute. Check merged pull request #3301 for the resolution; done means the intended module and test-specific process settings are applied without one unexpectedly overwriting the other.
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Assessment
- Domain
- build-system
- Issue type
- Bug
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 25/100