version 1.3.0

• Added a workflow for somatic SV calling using GRIDSS, delly and manta.
• Clever is now disabled by default. It can be enabled by setting SVcalling.runClever to true.
• Fixed a bug which led to the removal of all BND, INS and INV events if DUPHOLD was enabled.
• Updated SURVIVOR version to 1.0.7.
• Added a workaround for a bug in survivor which caused the END of events detected by CLEVER to be calculated
  incorrectly resulting in incorrect merging of events.
• The gridss outputs are now included in survivor as well.
• Smoove can now be disabled, by setting SVcalling.runSmoove to false.
• Added Gridss as SV caller.
• Fix order of input VCF files when removing missing and homozygous reference genotypes.
• Each SV type has now seperate temporary directory during sorting.
• Both union and intersection from each SV types are generated.
• The pipeline now first seperate SVs by types before merging.
• Duphold can now be run optionally to annotate and remove FP deletions and duplications.
• Replace excludeFpDupDel-option with runDuphold-option: DupHold annotation and FP filtering are now optional together.
• Update CLEVER dockerimage.
• DELLY: Update docker image.

Release 1.2.0

• Remove GRIDSS from the pipeline.
• Exclude GRIDSS from SURVIVOR merging: SVs were only defined as BNDs in GRIDSS.
• Optional filtering of missing and hom-ref genotypes.
• Optional filtering of FP deletions and duplications.
• Add DUPHOLD: annotate SVs with depth values.
• Make bcftools indexing optional.
• Structural-variantcalling pipeline: add sorting and change id.
• Added GRIDSS sv caller

Release 1.1.0

• Bcftools samtools and picard images are updated to newer versions.
• Bcftools view now converts delly vcf to a gzipped version.
• Tasks were updated to contain the time_minutes runtime attribute and
  associated timeMinutes input, describing the maximum time the task will
  take to run.

Release 1.0.0

First release of the structural variant calling pipeline.