Add paired-end test data, config profile, and CI matrix testing

[adamd3]

• Adds paired-end FASTQ Files (test_data) and paired-end Sample Sheet
• Adds paired-end test profile (test_pe.config & nextflow.config:82):
  • Created the -profile test_pe option to run paired-end tests cleanly: nextflow run BactSeq -profile test_pe,docker CI Testing Matrix (ci.yml:20-58):
• Adds paired-end test jobs to the GitHub Actions matrix for:
  • BWA (paired-end) on Nextflow 21.10.3
  • Kallisto (paired-end) on Nextflow 21.10.3
  • BWA (paired-end) on Nextflow 25.04.0