CI failure: OpenMS container cannot create config directory
- Dominant language
- Nextflow
- Stars
- 83
- Forks
- 57
- Avg merge
- 4h 14m
- Merged PRs (30d)
- 1
Description
## Bug
CI tests fail with:
```
filesystem error: cannot create directories: Permission denied [//.config/OpenMS]
```
This affects all OpenMS tools (e.g., `DecoyDatabase`) running in the `ghcr.io/openms/openms-tools-thirdparty:latest` container.
## Root cause
The container's `$HOME` resolves to `/` (root filesystem), and the new OpenMS version tries to create `$HOME/.config/OpenMS` on startup. The CI runner doesn't have write permission to `/.config/`.
## Impact
All quantms CI tests that use OpenMS tools fail before reaching any pipeline logic. This blocks all PRs from passing CI (e.g., #690).
## Reproduction
```
docker run ghcr.io/openms/openms-tools-thirdparty:latest DecoyDatabase --help
```
If `$HOME` is not set or is `/`, this will fail with the same permission error.
## Suggested fix
Either:
1. **In the container**: Set `HOME=/tmp` or `HOME=/home/openms` in the Dockerfile so `.config/OpenMS` can be created
2. **In quantms**: Set `HOME=/tmp` as an environment variable in the Nextflow process definitions
3. **In OpenMS**: Handle the case where `$HOME/.config` is not writable (fall back to `/tmp` or skip config creation)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Contributor guide
Assessment
This issue has not been assessed yet.