Version 19.10.1

• decrease default memory allocation to pack compute jobs tighter and increase pipeline throughput
• better handling for SLURM queue JSON
• remove all filters on variant output except PASS filters
• clean up 'work' directory upon successful pipeline completion
• add workflow completion status logging to make it easier to tell if workflow completed successfully
• fix issue with LofreqSomatic not outputting indels
• fix issue with masked nucleotides in variants breaking annotation merge script
• add annotation table comparison reporting to compare the outputs of different pipeline runs

Version 19.09.1

• split annotations.tsv output into paired and unpaired outputs
• add output backup recipes for Makefile
• minimum depth of coverage and filter changes for some variant caller outputs

Version 19.08.2

• increase Nextflow version to 19.07
• update Depth of Coverage analysis cutoffs
• several fixes to FACETS analysis steps
• fixes for SNP-pileup steps used for FACETS
• disable Varscan2 variant calling
• update Strelka variant filtering and fixes to vcf table conversion script
• add post-filter steps to further filter variants after annotation steps
• update 'submit' methods in Makefile to use new created SLURM submit script for Big Purple
• update 'submit' methods in Makefile to be compatible with SLURM scancel pipeline cancellation method
• remove dbSNP filtered variants from LoFreqSomatic output

Version 19.08.1

• add karyotype plots to report

• disable Pindel due to computational resource requirements

• return all transcripts from ANNOVAR annotations

Version 19.07.3

• add process ID reporting to pipeline to make it easier to stop submitted pipeline

• update CNV-Pool analysis for all samples in pipeline

• add 629 annotated targets .bed file

• fix ref dir parameter in cnv_pool workflow

Version 19.07.2

• fix errors in FACETS processing
• add Pindel indel calling

Version 19.07.1

• add Strelka for indel calling
• add FACETS for cnv calling

Version 19.05.4

• Added IGV Snapshots

• Fixed variant caller type labels throughout the pipeline

• cleaned up configurations code and moved more configs to the config.json for easier access

Version 19.05.3

• Added CNV Pool comparison

• Added CNV Pool reference file generation workflow

• Increased SLURM timeout

• Cleaned up some decimal values in reports

Version 19.05.2

• refactor targets .bed files and add support for alternative targets .bed files