CHANGELOG.md

v.2.0.1 (indev)

User Facing

• Corrected spelling of inferred (#125)
• Add param for seqwho reference (#127)
• Remove tracking param and all tracking code

Background

• Corrected file search parameters due to name inconsistency (#129)
• Re-implemented sym-link for deriva cookie into ~/.bdbag/ for bdbag fetch to use (#132)
• Add CI variables for staging RIDs (#133)
• Use CI staging RIDs for CI unit tests: getBag, uploadInputBag, uploadExecutionRun, uploadQC, uploadProcessedFiles, uploadOutputBag (#133)
• Add -u "F" to CI unit test uploadOutputBag upload_output_bag.py
• Remove "fail" integration CI tests (#133 addendum)
• Add licence header to nf file, R and python scriptsand pytest scripts
• Stop using RCB and RMB (default) with deriva.core insert calls to match server update (#134)
• Replace default seqwho reference location to one provided by source lab (#127)
• Update NF Tower access token to BICF user
• Disable NF Tower

v2.0.0

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
• Add seqtk to references
• Update software versions to latest (containers)

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• Remove check for multiple fastq check in parse metadata (redundant and no longer valid)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
• Change ambiguous species ci to wrong species
• Add test for DNAnexus env
• Add test for AWS env
• Fix fetch fastq count
• Fix failPreExecutionRun error collection