Tiger rattlesnake

• MAJOR CHANGES:

  • Allele-Specific mapping : Allele-specific DNA and RNA-mapping is now possible and both ChIP-Seq and RNA-seq pipeline can handle "allele_mapping" mode.
  • Differential binding : Differential binding can be performed using CSAW, both normal and allele-specific.
  • MultiQC : MultiQC summarizes QC results for DNA-mapping and RNA-mapping workflows.
  • R package : New R package called snakediff contains all functions for differential binding and expression. The DE functions have been
    transformed into clean and consistent layout, with docs.
  • Deeptools commands : All deeptools commands now moved into common deeptools_cmds module, and are shared between functions.

• MINOR CHANGES:

  • Wrappers have been formatted for easier readability.
  • chr X, Y, M and unmapped scaffolds are now ignored for normalization in bamCoverage (DNA-mapping) and bamCompare (Chip-Seq).
  • bamCompare outputs are named with suffix , instead of a static suffix "Input", this allows the workflow to run with different controls
    eg. Input, H3 and keep results in same dir. However, MACS2 would still over-write the output files from previous run (needs fix).
  • All code should be python3 compatible now
  • Code conforms to PEP8 and this is finally tested on travis-ci