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  • 0.0.4_indev
  • 0.0.3
    Release 0.0.3

    v0.0.3

    User Facing

    • TPM table:
      • Add Ensembl Gene ID
      • Rename columns: GENCODE_Gene_Symbol, Ensembl_GeneID, NCBI_GeneID
    • MultiQC output custom tables (html+JSON):
      • Run table: Session ID and Pipeline Version
      • Reference Table: Species, Genome Reference Consortium Build, Genome Reference Consortium Patch, GENCODE Annotation Release (outputs both human and mouse versions)
    • Add inputBag override param (inputBagForce) [*.zip]
      • Uses provided inputBag instead of downloading from data-hub
      • Still requires matching repRID input param
    • Add fastq override param (fastqsForce) [R1,R2]
      • Uses provided fastq instead of downloading from data-hub
      • Still requires matching repRID input param and will pull inputBag from data-hub to access submitted metadata for reporting
    • Add species override param (speciesForce) [Mus musculus or Homo sapiens]
      • forces the use of the provided species
      • ignores inferred ambiguous species

    Background

    • Add GeneSymbol/EnsemblID/EntrezID translation files to references

    Known Bugs

    • outputBag does not contain fetch for processed data
    • Does not include automatic data upload
    • Override params (inputBag, fastq, species) aren't checked for integrity
  • 0.0.2
    Release 0.0.2

    v0.0.2

    User Facing

    • Output:
      • inputBag
      • outputBag
    • Remove gene details from tpm table
    • Add EntrezID translation to tpm table (from version specific reference)

    Background

    • Add GeneSymbol/EnsemblID/EntrezID translation files to references

    Known Bugs

    • outputBag does not contain fetch for processed data
    • Does not include automatic data upload
  • v0.0.1
    Release v0.0.1

    INITIAL BETA VERSION

    Does not include automatic data upload
    This version is for initial upload of test data to GUDMAP/RBK data-hub for internal integration

  • aws
    da9ba44f · Remove trackStart ·