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Add --local option to Bismark Bowtie2 Wrapper (continuation from PR #1537) #1539

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jonasbucherETH
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This PR continues from PR #1537:

  • Add --local option to Bismark Bowtie2 Wrapper
  • update requirement versions
  • handle lint warnings

@bgruening
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This seems to be in the root folder, but it should be in the tools/bismark folder.

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