order of operations.md

• io-worker:
  • parse FASTQ
  • put reads into channel
• processing worker
  • align 3p linker
  • test isContaminant?
  • if yes:
    • align again
    • test again
  • if no:
    • put final read in read structure
    • put into output channel
• io-worker
  • take final read structure:
    • extract data and write to file
    • extract data and write to file