call-gSNP v9.0.0

CHANGELOG

Added

• Option for YAML input
• Record deduplication workflow

Changed

• Reorganize repo with pipeline entrypoint at root of repo and singular directory names

Fixed

• Bug with records being duplicated through the parallelized processing of BAMs (#79)

call-gSNP v8.0.0

CHANGELOG

Added

• BETA: Support for paired inputs with a single normal sample and multiple tumour samples

Changed

• Switch to SAMtools for indexing BAMs
• Use sample ID and intervals as identifiers for log output directories
• Standardize config structure
• Partially revert BQSR parallelization and group ApplyBQSR by interval
• Parallelize BaseRecalibrator per sample
• Save VQSR output for QC
• Save SNP+INDEL VQSRed VCF to output

call-gSNP v7.2.1

CHANGELOG

Changed

• Parallelize BQSR
• Update .gitignore

Security

• Update GATK to 4.2.4.1 to address Log4j vulnerabilities (GHSA-8489-44mv-ggj8, GHSA-p6xc-xr62-6r2g)
• Update Picard version to 2.26.10 to address Log4j vulnerabilities (GHSA-8489-44mv-ggj8)

call-gSNP v7.2.0

CHANGELOG

Changed

• Enable threading for MergeSamFiles
• Parallelize reheadering and indexing processes
• Update reheadering to use -c option
• Modularize workflows for different modes (single vs. paired, WGS vs targeted)
• Update GATK to 4.2.4.0 to address Log4j critical vulnerability (GHSA-jfh8-c2jp-5v3q)
• Update Picard to 2.26.8 to address Log4j critical vulnerability (GHSA-jfh8-c2jp-5v3q)

call-gSNP v7.1.0

CHANGELOG

Added

• Parallelize IR and BQSR in WXS/WES mode

Fixed

• Fix targeted, single sample mode bugs

call-gSNP v7.0.0

CHANGELOG

Added

• Update call-gSNP to DSL2
• Add GPL2 license
• Parallelize MergeVcfs
• Parallelize MergeSamFiles
• Standardize output and log directories
• Add process to remove intermediate files when save_intermediate_files is disabled
• Parallelize GetPileupSummaries, CalculateContamination, and DepthOfCoverage processes
• Split HaplotypeCaller process into process for VCF and GVCF modes
• Parallelize GVCF HC process
• Extract genome intervals from reference dictionary

Changed

• Adjust static resource allocation to be more efficient
• Auto-detect reference fasta dictionary
• Rename ".bai" output files to ".bam.bai"
• Auto-detect when in targeted mode and when in WGS mode

call-gSNP-DSL2 v7.0.0-rc1

CHANGELOG

Added

• Update call-gSNP to DSL2
• Add GPL2 license
• Parallelize MergeVcfs
• Parallelize MergeSamFiles
• Standardize output and log directories
• Add process to remove intermediate files when save_intermediate_files is disabled
• Parallelize GetPileupSummaries, CalculateContamination, and DepthOfCoverage processes
• Split HaplotypeCaller process into process for VCF and GVCF modes
• Parallelize GVCF HC process

Changed

• Adjust static resource allocation to be more efficient
• Auto-detect reference fasta dictionary
• Rename ".bai" output files to ".bam.bai"

call-gSNP-DSL2 v1.0.0-rc1

CHANGELOG

Added

• Update call-gSNP to DSL2