version 3.2.0

• Updates for miniwdl compatibility

Release 3.1.0

v3.1.0

Release 3.1.0

Release 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.

Release 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.

v1.0.0: version 1.0.0

version 1.0.0

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