@ewels ewels released this Dec 12, 2018

Assets 2

Pipeline updates

  • Removed some outdated documentation about non-existent features
  • Config refactoring and code cleaning
  • Added a --fcExtraAttributes option to specify more than ENSEMBL gene names in featureCounts
  • Remove legacy rseqc strandRule config code. #119
  • Added STRINGTIE ballgown output to results folder #125
  • HiSAT index build now requests 200GB memory, enough to use the exons / splice junction option for building.
    • Added documentation about the --hisatBuildMemory option.
  • BAM indices are stored and re-used between processes #71

Bug Fixes

  • Fixed conda bug which caused problems with environment resolution due to changes in bioconda #113
  • Fixed wrong gffread command line #117
  • Added cpus = 1 to workflow summary process #130