v2.0.1

Summary
Update to v2.0.0 of the app to robustly handle uploading job outputs and add compression of final intermediate VCFs

Changes

• fix for more robustly handling uploading job outputs due to bug in dx-jobutil-add-output
• add parallelised compression of final intermediate VCFs

Fixes
#19
#18
#20

v2.0.0

Summary

Refactor of v1.2.0 of the app to reduce run time through use of scatter gather in sub jobs, faster download / upload of files and making distinct output fields by file types to allow for easier downstream access to the output files.

Changes

• Refactor of app running to run per sample analysis in parallel in sub jobs, then final gather step in parent job to generate results output

  • Run time reduced for SP flowcell from 11-14 hours to <3 hours

• Faster downloading and uploading of files through parallelised functions

• Additional optional inputs added:

  • -iinclude_samples / -iexclude_samples - allows for including / excluding specific samples from analysis
  • -iscatter_instance - allows for overriding the default instance type set for the per sample scatter jobs
  • -iupload_demultiplex_output - allows for controlling if to upload the demultiplexing output along with the analysis output

• Distinct app output fields instead of a single array of files for the following:

  • fastqs
  • stitchedRealigned DNA bams
  • RNA bams
  • gVCFs
  • CNV VCFs
  • splice variant VCFs
  • MSI metrics
  • TMB metrics
  • variant annotation JSONs
  • CombinedVariantOutput tsvs
  • final metricsOutput tsv

Fixes

• Specify fastqs as ouput so it can be pulled out into a workflow #4
• Add priority flag in dxapp.json #5
• Link to Illumina documentation is invalid #7

v1.2.0

Initial production ready release.

The app was refactored from v1 to do the following:

• Accept fastqs as input to start analysis
• Have demultiplex only option to obtain fastqs
• Make the SampleSheet input optional to enable automation
• Have some better error handling for wrong or missing samplesheets.