v3.2.0

• Added the shallow input to enable shallow mode. Defaults to false.
• Added the runPolyGTrimming input to control whether or not poly-
  G-tail trimming should be performed by fastp. By default fastp's
  default behaviour will be used, ie. enabled for NextSeq/NovaSeq data
  as determined from the FastQ headers.
• Added the mappingThreads input to control the number of threads
  used per BWA mem job. Defaults to 8.
• Added the splitFastq input to control whether fastq files should
  get split into chunks or not. Defaults to true.
• Added the filterFastq input to control whether fastq files should
  get filtered on quality and read length prior to mapping. Default to
  true.
• Added the fastpCorrection input to control whether fastp's
  correction should be enabled. DEfaults to true.

v3.1.1

• Fixed an error in sortReportedVcf caused by an incomplete VCF header.

v3.1.0

• Added a task to call genotypes for specific sites.

v3.0.3

• runAdapterClipping is now set to true by default.

v3.0.2

• Limit the number of chunks per fastq file to 16. Fastp will run into
  issues if the number of chunks is not divisible by the number of
  threads it uses, which is limited to 16 theads.
• Runtime attributes for Amber were adjusted:
  • memory increased from 70GiB (javaXmx: 64G) to 85GiB
    (javaXmx: 80G).
  • timeMinutes increased from 240 to 480.

v3.0.1

• Fixed an issue where fastp errors if the number of splits for
  a fastq file is set to 1.
• Fixed a bug that caused the header of the reportedVAR.vcf output to
  be malformed. (see v2.1.1)
• Memory requested for mark duplicate tasks increased from 25000 Mb to
  50000 Mb.

v2.1.1

• Fixed a bug that caused the header of the reportedVAR.vcf output to
  be malformed.

v3.0.0

• Use fastp for adapter clipping and initial QC metrics collection
  instead of the biowdl QC workflow (which uses cutadapt and fastqc).
  Also replaces fastqsplitter for chunking of the fastq files.
• Added picard CollectInsertSizeMetrics.
• Added MultiQC.
• Increased the number of threads used for duplicate marking to 8 (was 3).

v2.1.0

• Added a task that generates a table of VAFs (as determined by Purple)
  for somatic variants.
• Added an output stating the pipeline version.
• Removed unused breakpointHotspot input.
• Removed unused peachTranscriptTsv input.
• Removed unused import of snpEff task.
• Chunk numbers per input fastq are now calculated based on size.
  The total number of chunks can be set using the
  totalMappingChunks inputs, which defaults to 25.
• For various jobs the default runtime attributes have been adjusted
  to be more efficient.

v2.0.0

• Tool versions were upgraded:
  • Cuppa: 1.4 -> 1.6
  • Gripss: 1.11 -> 2.0
  • Linx: 1.16 -> 1.18
  • Protect: 1.4 -> 2.0
  • Purple: 3.1 -> 3.2
  • virus-interpreter: 1.0 -> 1.2
  • Peach: 1.0 -> 1.5
• snpEff was replaced with Pave.
• LinxVisualization was added.
• CupGenerateReport was added.
• Orange was added.
• Added a job to create a VCF of reported variants.