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Published December 12, 2018 | Version 1.2
Software Open

nf-core/rnaseq: nf-core/rnaseq version 1.2

Creators

  • 1. Science for Life Laboratory
  • 2. @qbicsoftware
  • 3. Inivata
  • 4. @SciLifeLab | Karolinska Institutet
  • 5. @NationalGenomicsInfrastructure @SciLifeLab
  • 6. QBiC @qbicsoftware
  • 7. Comparative Bioinformatics, CRG
  • 8. Genome Institute of Singapore
  • 9. University of Copenhagen
  • 10. National Genomics Infrastructure, Science for Life Laboratory

Description

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  • Removed some outdated documentation about non-existent features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

Files

nf-core/rnaseq-1.2.zip

Files (4.0 MB)

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md5:5c3f95e22009746730cc5132170703fc
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Additional details

Related works

Is supplement to
https://github.com/nf-core/rnaseq/tree/1.2 (URL)