Genomic Sequence Batch Alignment Workflow Management

Create a sophisticated Bash script for managing large-scale genomic sequence alignment workflows using BWA and GATK. The script should: 1) Automatically detect and validate input FASTQ files, 2) Dynamically allocate CPU cores based on system resources, 3) Implement a queuing mechanism for multi-sample processing, 4) Generate comprehensive alignment quality reports, 5) Support multiple reference genome configurations. Include advanced logging, error recovery, and the ability to resume interrupted jobs.