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Remove check for multiple fastq check in parse metadata (redundant and no longer valid)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