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- Remove check for multiple fastq check in parse metadata (redundant and no longer valid)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