Changelog

version 3.2.0

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.

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.