CHANGELOG.md

v0.1.0 (in development)

User Facing

• Add option to pull references from datahub
• Add option to send email on workflow error, with pipeline error message
• Add versions and paper references of software used to report
• Upload input bag
• Upload execution run
• Upload mRNA QC
• Create and upload output bag
• Add optional to not upload

Background

• Remove (comment out) option to pull references from S3
• Make pull references from BioHPC default (including in biohpc.config)
• Start using new gudmaprbk dockerhub (images autobuilt)
• Moved consistency checks to be fully python
• Changed order of steps so that fastqc is done after the trim step

Known Bugs

• Datahub reference pull uses dev.gudmap.org as source until referencencs are placed on production
• outputBag does not contain fetch for processed data
• Does not include automatic data upload
• Override params (inputBag, fastq, species) aren't checked for integrity

---

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

---

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

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

---