Resolve "process_align"

Alignment step using HiSat2

PR checklist

• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
• README.md is updated

• Close issue
  Closes #4 (closed) Addresses alignData: add samtools to convert sam to bam and sort from #21 (closed)

/cc @ghenry @venkat.malladi /assign @ghenry