v2.0.0rc01

User Facing

  • Endness metadata "Single Read" changed to "Single End" in data-hub, pipeline updated to handle (#110) ("Single Read" still acceptable for backwards compatibility)
  • Strandedness metadata "yes"/"no" changed to boolean "t"/"f" in data-hub, pipeline updated to handle (#70) ("yes"/"no" still acceptable for backwards compatibility)
  • Upload empty mRNA_QC entry if data error (#111)
  • Allow forcing of strandedness and spike (#100)

Background

  • Add memory limit (75%) per thread for samtools sort (#108)
  • Remove parsing restrictions for submitted stranded/spike/species (#105, #106)
  • Pass unidentified ends instead of overwriting it as unknown
  • Move fastqc process before trim to catch fastq errors (#107)
  • Only use fastq's that match *[_.]R[1-2].fastq.gz naming convention (#107)
  • Add error output for no fastq's
  • Update input bag export config to only fetch fastq's that match *[_.]R[1-2].fastq.gz naming convention
  • Remove check for multiple fastq check in parse metadata (redundant and no longer valid)
  • Handle blank submitted endness better
  • Don't use file.csv from inputBag to parse manual endness, use counted from getData
  • Detect malformed fastq's (#107)
  • Restrict sampled alignment process to use >32GB nodes on BioHPC (#108)
  • Use nproc**-1** for alignment processes (#108)
  • Data-hub column title change from "Sequencing_Type" to "Experiment_Type" (#114)
  • Data-hub column title change from "Has_Strand_Specific_Information" to "Strandedness" (#115)
  • Merge data error pre-inference execution run upload/finalize to 1 process
  • Change uploadOutputBag logic to change reuse hatrac file if alread exists (re-uses Output_Bag entry by reassigning Execution_Run RID) (#112)
  • Add new CI py tests for override and integration

Known Bugs

  • Override params (inputBag, fastq, species) aren't checked for integrity
  • Authentication files and tokens must be active (active auth client) for the duration of the pipeline run (until long-lived token utilization included)
  • Check for outputBag in hatrac doesn't check for any uploaded by chaise