Release 4.0.0

• Default docker images for various tools have been updated.
• Changes in Cromwell 48 made it impossible to use the wide array of inputs
  in our documentation (such as
  RNAseq.sampleJobs.qc.Cutadapt.minimumLength). Fixes have been made
  upstream and in the pipeline. From Cromwell 52 onwards these options will be
  available again.
• Bam files are no longer indexed after alignment, saving compute time.
• WDL files and imports zip packages are now provided each release to make
  running pipelines easier.
• The output directory was simplified. All files related to a sample are now
  in the samples/<sample_id> directory.
• Use the scatter-regions tool to replace biopet-scatterregions.
• The pipeline was renamed from "pipeline" to "RNAseq".
• Tasks were updated to contain the time_minutes runtime attribute and
  associated timeMinutes input, describing the maximum time the task will
  take to run.
• Added a step to generate the STAR index, if neither a STAR nor a Hisat2 index
  is provided.
• Document the use of cromwell's final_workflow_outputs_dir feature which
  makes the RNA-seq pipeline usable on all of Cromwell's supported backends.
  Users are encouraged to use this feature. outputDir references are
  removed from the documentation.
• Make the MultiQC task suitable for use with a final_workflow_outputs_dir
  so it can be used on all of Cromwell's supported backends.
• Added a picard markduplicates step after UMI deduplication.
• Move common optional inputs to top-level workflow, so nested inputs are not
  required anymore for the majority of configurations.
• The pipeline has been altered so it starts the variant calling jobs in a more
  efficient way.
• Major bug fix: The --dont-use-soft-clipped-reads is now used on
  HaplotypeCaller in concordance with GATK best practices.