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v0.26.0
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@cflerin cflerin released this 01 Jul 14:49
· 236 commits to master since this release
v0.26.0
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Summary of changes

  • File converter cleanup (py, R)
  • Use multiple batch variable for harmony (#297)
  • Add harmony/scenic workflow (#312)
  • Additional arguments possible for harmony (#313)
  • Fix reproducibility of cell normalization (#295)
  • Fix bugs in scrublet (#306, #308)
  • Cell annotation filter fixes (#309)
    • Allow metadata to match to fewer than the full set of barcodes in the
      adata object (80% or more cells allowed)
    • Add CI test for cell annotation method
  • Add quiet mode (#305)
  • Cellranger updates (#304) and profile updates (#320)
  • Remove exception on Scenic multiruns that prevents the workflow running in a local executor
  • Remove hard links from the publishing process (#318)
  • getDataChannel updates:
    • Implement file tagging (#291)
    • Fixes to account for the tag parameter in the remaining file types
    • Bugfix for parsing multiple paths separated by a comma
  • Popscle (freemuxlet/demuxlet) workflow updates (#330)
    • Allow input files (bam, barcodes) other than those from Cellranger formatted sources
    • Allow analysis on barcodes other than 'CB'
  • Add VSC/HPC specific config
  • Docker image updates
    • Include samtools and a base image with zlibng for faster compression/decompression (#325)
    • Use this base image for other tools (popscle, bwamaptools, singlecelltoolkit, ...)
  • Documentation updates
  • Fix incorrectly applied compute resources settings (#335)

Updates to scATAC-seq preprocessing v1 (#334)

  • Update bwa mapping approach
    • skip samtools sort step, turn off compression for piped commands, reduce samtools threads
    • Re-work add_barcode_as_tag mawk script to include both corrected and uncorrected barcode tags in final bam
    • Split bwamaptools config file into discrete parts that can be loaded separately
  • Update fragments sorting command with locale
  • BAP updates
    • Implement multiplet detection pipeline
    • Add ipynb report to summarize bap results
    • Fix bap install in Docker image
  • Enable skipping of barcode correction (when whitelist parameters are empty)
  • scATAC-seq docs updates and fixes
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