Release_4.0.0: Merge pull request #28 from DKFZ-ODCF/pre-release-4

• major: resources/configurationFiles/analysisRNAseq.xml is now just a default configuration with many configuration options left blank. For your <analysis> tags in your project XMLs the analysis names can be changed to use the following defaults:
  • GRCh37, mm10: RNAseqAnalysis
  • GRCh38-specific: RNAseqAnalysisGRCh38
• major: Update default software versions for all assemblies
  • Arriba 2.3.0
  • STAR 2.7.10a (from 2.5.3a for hg37/mm10 and 2.7.6a for hg38)
  • Kallisto 0.46.0 (from 0.42.0)
  • Samtools 1.9 (from 1.6)
  • HTSlib 1.9 (from 1.6)
  • subread 1.6.5 (from 1.5.1): The previous version produces occasional segmentation faults (related to extreme optimization option -O6) but otherwise produces the same results. Both versions produced exactly the same featureCounts in multiple tests.
• major: Gene model gencode version 39/43 was used to create the STAR and Kallisto indexes
• major: Update default paths to new ngs_share at ODCF.
• major: GRCh38 STAR and Kallisto indexes are based on refmake workflow.
• major: Updated the Conda environment.yaml.
  • Note for users at the DKFZ cluster: The software versions used in Conda environment do not exactly match the versions in the default configuration used for the cluster's module system.
• major: Column rename in featureCounts table:
  • "FPKM_no_mt_rrna_trna_chrxy{,_fw,_rv}" -> "FPKM_customLibSize{_unstranded, _stranded, _reverse_stranded}"
  • "TPM_no_mt_rrna_trna_chrxy{,_fw,_rv}" -> "TPM_customLibSize{_unstranded, _stranded, _reverse_stranded}"
  • "FPKM_standard{,_fw,_rv}" -> "FPKM{_unstranded, _stranded, _reverse_stranded}"
  • "TPM_standard{,_fw,_rv}" -> "TPM{_unstranded, _stranded, _reverse_stranded}"