v0.26.1

• Fix the demultiplexing of run with mixed barcode length across lanes

v0.26

• Switch from using clarity REST API to using Reporting LIMS endpoints wherever possible
• Split demultiplexing per lane and allow for non pooling lane to be sequenced in pooling run.
• Fastq-Filterer applied to intermediate fastq files before alignment.
• Project process now use GATK4 for trio check

v0.25.3

• Fix fastqc command to set the temp directory to lustre.

v0.25.2

• New toolset for non human variant call with GATK3.8
• Support for Asana API changes

v0.25.1

• Fixed IDT barcode support
• 'gender' API key renamed to 'sex'

v0.25

• New pipelines :
  • GATK4 based QC and variants call for human and non-human samples
  • Dragen based variant call for human sample starting from the run processing
• New Features:
  • file program_version.yaml only records version of tools used by the pipeline
  • Location of genome on the filesystem is provided by the REST API
  • Genome used during Sample processing is uploaded to the REST API
  • Demultiplexing support IDT barcodes
  • Sample Processing will start coverage from run elements is greater than required coverage
  • analysis_driver.log only contains info level logs. New log containing debug level in analysis_driver-debug.log
• Bug fixes:
  • Interop metrics parser doe not uploade NaN
  • Check that all bcl files are present before starting run processing
  • Java tools version can now be determined in cron
  • Increase memory available for trio checking for projects with more than 25 samples

v0.24.1

• Bugfix: ensure the bcls expected to exist exists before returning a completed cycle with interop
• Bugfix: make the samplesheet deterministic and only generate it when required

v0.24

• Alignment during run processing start after the 50 cycles into read2 to speed up alignment metric generation
• Run picard GC bias detection tool anc calculate new metric to summarise each run element's GC-biais
• Update Picard to version 2.18.23
• Update bcl2fastq to version 2.20
• Bugfix: Initialise analysis_driver_procs at the start to avoid missing embedded entities
• Bugfix: Exceptions raised in Luigi are propagated to the main thread

v0.23.1

• Updated EGCG-Core to 0.9.1

v0.23

• Location-independent integration testing with EGCG-Core
• Updated EGCG-Core to v0.9
• Only running trio check on valid projects
• Fixed memory allocation for indel realignment and GenotypeGVCFs
• Eager-loading output config file
• Removed usages of old aggregation
• Overwriting existing fastqs in SampleDataOutput
• Minor fixes: rerunnable stages, pipeline start date, FR insert metrics, PhiX error handling