bigbio / bigbio/quantms

CI failure: OpenMS container cannot create config directory

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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)

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