1.4.0

• Updated to dsde-pipeline workflow version 2.0.1
  • Remove GetBWAVersion as a task and moved it to SamToFastqAndBwaMemAndMba
• Add more description for workflow in ReadMe

1.3.0

• Updating workflow to 2.0v
  • Changes to the inputs included with the dna seq single sample references struct:
  • Removed 'fingerprint_genotypes_file' and 'fingerprint_genotypes_index' from bundle and made these optional pipeline inputs
  • Removed 'haplotype_scatter_count' and 'break_bands_at_multiples_of' from bundle and added these to a separate 'VariantCallingScatterSettings' struct
  • Added 'haplotype_database_file' to the references bundle as a non-optional file
  • Renamed GermlineSingleSampleReferences to DNASeqSingleSampleReferences
  • Updated shared tasks to support the new TargetedSomaticSingleSample pipeline
• Removed import urls and left in the local directory paths, because Dockstore/Terra can now handle relative import paths.
• Increased the disk multiplier in SortSam task from the original dsde-pipeline from 3.25 to 6.25, in order for the workflow to run on Terra. Reason for this change is due to the difference in PAPI version being used in Terra vs prod.

1.2.0

1.3

• Modified the ExomeGermlineSingleSample pipeline to use an up-to-date set of contamination resource files for VerifyBamId. Further, these contamination resource files are subsetted by the target interval list.
• Removed unused import statements from ExomeGermlineSingleSample.wdl
• Also includes previous version updates:
  • 1.2
    • Adjusted memory parameters to avoid Google's new e2 instances because there are not enough machines to satisfy our production use case.
  • 1.1
    • This is an update to the ExomeGermlineSingleSample pipeline. We are jumping forward several versions of Picard, from version 2.18.27 to 2.20.4

1.1.0

Updated scripts to match dsde-pipelines repository. See PR for details of changes here

1.0.0

Initial release of the Exome Analysis Pipeline.
This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and Indel discovery in human exome sequencing data.