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nf-core/rnaseq: nf-core/rnaseq version 1.3

Phil Ewels; Rickard Hammarén; Alexander Peltzer; Denis Moreno; rfenouil; Maxime Garcia; Senthilkumar Panneerselvam; marchoeppner; Sven F.; jun-wan; Johannes Alneberg; aanil; Sofia Haglund; Paolo Di Tommaso; Anders Jemt; KochTobi; Lavanya Veeravalli; Colin Davenport; Rad Suchecki; Max Natthawut Adulyanukosol; Francesco; Denis OMeally; Chuan Wang

Pipeline Updates

  • Added configurable options to specify group attributes for featureCounts #144
  • Added support for RSeqC 3.0 #148
  • Added a parameters.settings.json file for use with the new nf-core launch helper tool.
  • Centralized all configuration profiles using nf-core/configs
  • Fixed all centralized configs for offline usage
  • Hide %dup in multiqc report
Bug fixes
  • Fixing HISAT2 Index Building for large reference genomes #153
  • Fixing HISAT2 BAM sorting using more memory than available on the system
  • Fixing MarkDuplicates memory consumption issues following #179
Dependency Updates
  • RSeQC 2.6.4 -> 3.0.0
  • Picard 2.18.15 -> 2.18.23
  • r-data.table 1.11.4 -> 1.12.0
  • r-markdown 0.8 -> 0.9
  • csvtk 0.15.0 -> 0.17.0
  • stringtie 1.3.4 -> 1.3.5
  • subread 1.6.2 -> 1.6.4
  • gffread 0.9.9 -> 0.9.12
  • multiqc 1.6 -> 1.7

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