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@naumenko-sa naumenko-sa released this 14 Apr 13:29
· 161 commits to master since this release
v1.2.8
e1192f4
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Learn about vigilant mode.
  • Set ENCODE library complexity flags properly for ChIP-seq. Thanks to @mistrm82.
  • Fix greylisted peaks not being propagated to the output directory. Thanks to @mistrm82.
  • Better error message when no sample barcodes are found for single-cell RNA-seq.
  • Better trimming for 2 wgbs kits
  • enable setting parameters for deduplicate_bismark
  • custom threading for bismark via yaml
  • reproducible WGBS user story with the data from Encode
  • While consensus peak calling, keep the highest scoring peak instead of calling the summit for the highest scoring peak and expanding the peak to 250 bases.
  • Enable consensus peak calling for broad peaks. Thanks to @mistrm82 and @yoonsquared for pointing out this was missing.
  • Re-enable ATAC-seq tests, they work now.
  • svprioritize for mm10
  • purecn_Dx.R - mutational signatures - still requires a manual update of deconstructsigs or release of it
  • make sure purecn uses sv_regions bed to call variants
  • fix misleading disambiguation fastqc read statistics (total, hg38, mm10)
  • wgbs: nebemseq kit: add --maxins 1000 and --local to bismark align
  • WGBS: sorted indexed deduplicated bam for ready.bam
  • print error message when aligner: false and hla typing is on
  • make sure that mark_duplicates is false with collapsed UMI input
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