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run.py needs to be updated #5

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dacb opened this issue Jul 10, 2019 · 1 comment
Open

run.py needs to be updated #5

dacb opened this issue Jul 10, 2019 · 1 comment
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@erinhwilson

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@dacb
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dacb commented Jul 10, 2019

Issues noticed by @dacb and @erinhwilson:

  • During indexing of the bam file, the .sorted.bam is appended twice to the file name
  • When run in output as scripts mode, the faidx and file removal commands are not saved in the script
  • When run in output as scripts mode, the faidx command should not be run
@dacb
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dacb commented Jul 16, 2019

Additional opportunities:

  • The parallelization engine does the jobs for each step in parallel then moves to the next step. This assures the operations on any file are atomic, but it causes a condition where the paralyzation engine is not fully loaded.

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