align-DNA v8.0.0

Changed

• Update .gitignore file according to template
• Standardize output and log directory structure
• Update index file extension from all processes to .bam.bai
• Standardize config files
• Remove spark_temp_dir parameter from config template
• Replace temp_dir parameter with work_dir parameter

Added

• Intermediate file removal
• Spark tempdir permission checks

Full Changelog: v7.3.1...v8.0.0