CHANGELOG.md

v2.0.0rc02

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)
• Add seqwho
• Add seqwho results to multiqc report
• Modify repository structure to allow for use with XPACK-DNANEXUS
• Add override for endness

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• Remove check for multiple fastq check in parse metadata (redundant and no longer valid)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
• Fix fastq file and species error status detail bub (#118)
• Make compatible with XPACK-DNANEXUS
• Don't download fastq's if fastq override present
• Override fastq count to override counts

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

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v1.0.2

User Facing

Background

• Fix spelling in config file for process of failed fastq to upload error message (#104)

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)

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v1.0.1

User Facing

Background

• Split non-metadata mismatch error handling proces into 2, 1 to handle fastq errors and one for species errors (BUG FIX #101)
• Add known errors to integration CI tests (ambiguous species, trunkated fastq, R1/R2 mismatch (#103)
• Fix pre exeuction run fails uploading of execution run RID to tracking site (#96, #97)
• Change CI replicate count badge CI to count all execution runs that match major version

Known Bugs