CHARLIE 0.11.1

• CHARLIE was falsely throwing a file permissions error for tempdir values containing bash variables. (#118, @kelly-sovacool)
• Singularity bind paths were not being set properly. (#119, @kelly-sovacool)
• Update docker containers to set $PYTHONPATH. (#119, #125, @kelly-sovacool)
  • Otherwise, this environment variable can be carried over and cause package conflicts when singularity is not run with -C.
  • Also use python -E to ensure the $PYTHONPATH is not carried over. (#129, @kelly-sovacool)
• Fix reconfig to correctly replace variables in the config file. (#121, @kelly-sovacool)
• Prevent using excessive memory when copying reference files. (#126, @kelly-sovacool)
• Fix missing output files due to file system latency and use real (absolute) paths where possible. (#130, @kelly-sovacool)
• Update documentation to reflect biowulf usage and improved test dataset. (#132, @kelly-sovacool)