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This repository has been archived by the owner on Jan 5, 2021. It is now read-only.

Releases: gatk-workflows/gatk4-genome-processing-pipeline

1.3.0

07 Oct 13:52
@bshifaw bshifaw
1.3.0
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1.3.0 Latest
Latest

  • Updated wdls to match dsde-pipeline version 2.1.0:

    • Added a meta section with 'allowNestedInputs' set to 'true' to allow the workflow to use with nested inputs with Cromwell 52. (from 2.1.0)
    • Remove GetBWAVersion as a task and moved it to SamToFastqAndBwaMemAndMba. (from 2.0.1)

  • Edits to ReadMe

    • Specified GATK version used
    • Added note that repository will be archived and new location for workflows will be broadinstitute/warp
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1.2.0

22 Jul 13:22
@bshifaw bshifaw
1.2.0
adefba2
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1.2.0

Updated workflow to 2.0:

Breaking changes to the structure of pipeline inputs.

  • 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

Additional changes

  • Renamed GermlineSingleSampleReferences to DNASeqSingleSampleReferences
  • Updated shared tasks to support the new TargetedSomaticSingleSample pipeline
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1.1.0

23 Apr 19:38
@bshifaw bshifaw
1.1.0
a0a49d2
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1.1.0
  • Updated workflow to 1.4.
    • Added 'additional_disk' parameter to accommodate larger samples that have steps that run out of disk.
  • Reverted url imports to local imports
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1.0.0

26 Jan 01:09
@bshifaw bshifaw
1.0.0
cd1060b
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1.0.0

Initial addition of workflows used for germline processing in whole genome sequence data. This repo replaces the five-dollar-genome-analysis-pipeline repository. The workflows are the same with additional updates:

  • Modified the WholeGenomeGermlineSingleSample pipeline to use an up-to-date set of contamination resource files for VerifyBamId.
  • Removed unused import statements from WholeGenomeGermlineSingleSample.wdl
  • Adjusted memory parameters to avoid Google's new e2 instances because there are not enough machines to satisfy our production use case.
  • This is a major update to the WholeGenomeGermlineSingleSample pipeline. We are jumping forward several versions of Picard, from version 2.16.0 to 2.20.4
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