Skip to content

Latest commit

 

History

History
51 lines (45 loc) · 1.87 KB

CHANGELOG.md

File metadata and controls

51 lines (45 loc) · 1.87 KB
Raw

Changelog

version 3.0.0

  • Updated default images.
  • Estimate the time needed for each scatter by checking the size of the input BAM file.
  • Use scatter-regions to replace biopet-scatterregions. This allows the pipeline to work with scattersizes greater than 2 billion.
  • Added bcftools stats task to generate stats on called VCF files.
  • Tasks were updated to contain the time_minutes runtime attribute and associated timeMinutes input, describing the maximum time the task will take to run.
  • Refactoring of the pipeline:
    • Split up the pipeline into a single sample variant calling pipeline and a part that performs the joint genotyping. This allows for more elegantly integrating the pipeline into other pipelines.
    • Merge steps are only performed when there is more than one scatter. This prevents data from being written twice unnecessarily.
    • multisample-variantcalling.wdl is a reference implementation.

version 2.0.0

  • Add a scatterSizeMillions parameter to make it easier to set larger scatter sizes.
  • Multisample VCFs are only produced when joint genotyping is used.
  • Add option to output single-sample GVCFs
  • Make Joint Genotyping by GenotypeGVCF an optional step, so the pipeline can be used for RNA variant calling.
  • Make using a dbsnp VCF file optional.
  • Added gender-aware capabilities to the pipeline. This has changed the input format.
  • Added inputs overview to the docs.
  • Added parameter_mets.
  • Added wdl-aid to linting.
  • Added miniwdl to linting.

version 1.0.0

  • Combine the bam-to-gvcf and joint-genotyping pipeline into one.