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Overall optimizations #7

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johnegarza opened this issue Apr 16, 2019 · 0 comments
Open

Overall optimizations #7

johnegarza opened this issue Apr 16, 2019 · 0 comments

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@johnegarza
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  • bamtofastq output goes to /dev/null: why and should we stick to this
  • several steps use multiple cores: could/should we use more, make sure to keep requirements up to date in the cwl tool resource requirements field
  • how much memory should be requested overall?
  • should we output multiple solutions? Currently we only output the optimal/top hit, but there is an option to generate more
  • outputs are not as accurate as we hoped; can we changed the beta parameter to improve sensitivity, possibly in combination with the above suggestion
  • what is the "skip samse step"?
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