**PATCH** Update to Jaffa Parsing - Bump Docker to Python 3.12 - Correct "Directory not empty: 'tmp_dir'"

[MikeWLloyd]

Summary of changes

1. JAFFA parser updates

• Updated JAFFA parsing to support both legacy and newer JAFFA output headers.
• Updated JAFFA parsing to support both ":" and "::" gene name delimiters in fusion names.
• Added fallback handling for known status when the old known column is absent, using known mitelman and known cosmic fields.
• Added optional extraction of newer metadata fields when present, including geneCounts1, geneCounts2, known_mitelman, known_cosmic, cosmic_tier, and gtex_samples.
• Changes are in jaffa.py.

2. JAFFA test coverage updates

• Expanded parser tests to validate compatibility with both old and newer JAFFA formats.
• Added fixture coverage for new JAFFA headers and expected field mapping behavior.
• Changes are in test_jaffa_parser.py.

3. Dockerfile fixes and runtime compatibility improvements

• Updated base image to Python 3.12 slim to match package metadata and current code syntax requirements.
• Added WORKDIR /app so repository contents are copied into an application directory instead of filesystem root.
• Installed procps to provide ps, which is required by Nextflow task metrics collection.
• Kept sqlite3 installation and pip-based package install flow.
• Changes are in Dockerfile.

4. Fix for Directory not empty: tmp_dir
   Stated was fixed in [MAJOR] Update COSMIC API access, add createdb command, improve tests/docs, and remove unused sync #90, but I was still seeing the error in the most recent code base via the 3.12 docker container. So to fix:

• Hardened download cleanup logic so temporary directory handling is path-safe and idempotent.
• Avoided fragile cleanup behavior tied to relative working directories.
• Ensured cleanup runs from a stable cwd and tmp cleanup is done with absolute paths.
• Also aligned QIAGEN download function signature/call path in the same flow.
• Changes are in download.py and net.py.

Why this is needed

• JAFFA output format changes were causing a missing field to be extraction without compatibility handling.
• Docker builds and runtime behavior were impacted by older Python base usage and root-level copy behavior.
• Nextflow execution requires ps; missing procps caused runtime failures.
• Download workflow could fail during cleanup with Directory not empty: tmp_dir in containerized or repeated runs.

Validation performed

1. Verified fusion_report entrypoint works from a local Python 3.12+ virtual environment.
2. Confirmed CLI help command executes successfully.
3. Confirmed Dockerfile now uses application workdir and includes Nextflow-related ps dependency.
4. Confirmed cleanup code paths now use absolute paths and safer deletion behavior.

Notes

• This PR does not change report-generation semantics outside JAFFA field mapping compatibility and download cleanup robustness.
• Existing workflows using old erJAFFA output remain supported while adding support for newer JAFFA outputs.