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TODO.md

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TODO list

Mandatory

  • Documentation
  • Full scale test
  • get rid of negatively scored chains
  • Organise cat step better
  • Get rid of all magic numbers and strings
  • Check for output presence after each step
  • Nextflow manager class -> dedicated class for NF config
  • Double check the pipeline default parameters
  • Fix the install dependencies script
  • Logging messages
  • For all subprocesses -> error handling
  • Check for absent expected files

Nice to do

  • About dependencies: properly handle missing *.so error that may occur when running Kent binaries, like here #34
  • QC module: #33
  • lastz_q parameter - figure out what stands for and whether it is needed
  • Explanation for each pipeline parameter in the parse_args
  • Document masking, etc. - nuances that affect the pipeline performance.
  • Refactor HL kent dependencies -> maybe it was not necessary to split into 2 dirs? -> not split anymore
  • Refactor chain gap filler: get rid of chainExtractID dependency -> not needed
  • read parameters from config file
  • #20 - temp files location

Ideas for additional features

  • Self chains: #31

Very minor things

  • install_dependencies crash FileNotFoundError: [Errno 2] No such file or directory: 'wget' -> maybe show a better message suggesting to install wget?