CI failure: OpenMS container cannot create config directory

[ypriverol]

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)

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