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  • #33
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Issue created Aug 18, 2021 by Valentina Galata@valentina.galataMaintainer

SortMeRNA rule: minor bug and formatting

The current rule for rRNA filtering has a minor bug and could be reformatted for readability and code stability purposes.

Minor bug:

  • L15: should that not happen if the OTU file is absent? The -s flag tests for an existing and non-empty file.

Formatting suggestions:

  • avoid hard-coded paths
  • use keywords for input/output instead of indices
  • set parameters in the rule and not CMD if possible
  • simplify redirection of stderr/stdout into the log file; add logs created by the tools itself
  • use the option out2 to create separate PE FASTQ files instead of splitting the output later
  • use temp(...) for tmp files if possible
  • create unique tmp folders for working directories and clean up afterwards
  • since this is the only rule, include the CMD and parameters defined above the rule into the rule itself
  • add comments
Edited Aug 19, 2021 by Valentina Galata
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