v0.6.2

What's Changed

Bug fixes

• Remove calling of SV's in regions of interest only. Fixes #45

Full breakdown

• Release 0.6.2 by @leahkemp in #47

• Full Changelog: v0.6.1...v0.6.2

v0.6.1

What's Changed

New features

• Publish individual SNP/indel and SV VCF's in cohort/deeptrio mode

Bug fixes

• Fix sort of joint jasmine SV VCF, which affected the VCF header (order of VCF header and caused overwrite of jasmine INFO tags during downstream annotation)
• Strip prefixes jamines appends to sample ID's in joint SV VCF files

Other changes

• Add 'jasmine' in the joint SV VCF filename for clarity that it's a joint VCF
• Add more walltime for joint phase

Full breakdown

• Release 0.6.1 by @leahkemp in #44

• Full Changelog: v0.6.0...v0.6.1

v0.6.0

What's Changed

New features

• Add cohort (trio) analysis with DeepTrio (SNP's/indels) and Jasmine (SV's)
• Optimise DeepTrio thanks to Kisaru Liyanage @kisarur! Much speed, little SU cost!
• Make minimod haplotype aware
• Make minimod output bed and bigwig files
• Split multiallelic variants into biallelic variants
• Update SV caller (sniffles and cuteSV) versions (2.3.3 to 2.6.0 and 1.0.13 to 2.1.1 respectively)
• As a side effect of updating the SV callers, now SV's will be variant be called only within the regions of interest if a regions of interest file is provided)
• Allow base modification analyses to be optional

Bug fixes

• Add assumption that input data is in unaligned BAM (uBAM) format for base modification analyses. Fixes #38

Other changes

• Update nextflow version (24.04.1 to 24.04.4) - use the latest version available as an environmental module on NCI
• Inclusion of some un-reported software versions
• Minor improvements to documentation

Full breakdown

• Release 0.6.0 by @leahkemp in #37
• Full Changelog: v0.5.0...v0.6.0

v0.5.0

What's Changed

New features

• Add minimod

Other changes

• Minor changes to documentation

Full breakdown

• Release v0.5.0 by @leahkemp in #33
• Full Changelog: v0.4.2...v0.5.0

v0.4.2

What's Changed

New features

• Handle input SV VCF as a pipeline input (secret sauce/undocumented option)

Other changes

• Handle creating dummy NONE file for optional pipeface inputs within pipeline which enables running pipeline from remote directories
• Minor changes to formatting of reported in_data format in pipeface_settings.txt files
• Minor changes to documentation
• Minor changes to code comments
• Minor changes to error messages
• Fix input tuples for vep_sniffles_sv and vep_cutesv_sv processes

Full breakdown

• Release v0.4.2 by @leahkemp in #31
• Full Changelog: v0.4.1...v0.4.2

v0.4.1

What's Changed

Bug fixes

• Fixes #26

Full breakdown

• Release v0.4.1 by @leahkemp in #28
• Full Changelog: v0.4.0...v0.4.1

v0.4.0

What's Changed

New features:

• Change output directory structure to align with internal needs and in preparation for adding cohort analysis

Other changes:

• Simplify input/output tuples throughout the pipeline
• Other minor modifications to formatting/syntax/grammar

Full breakdown

• Release v0.4.0 by @leahkemp in #25
• Full Changelog: v0.3.0...v0.4.0

v0.3.0

What's Changed

New features:

• Structural variant annotation (hg38 only)

Other changes:

• Set the minimum length of SV's during variant calling to 50
• Minor changes to documentation

Full breakdown

• Release v0.3.0 by @leahkemp in #23
• Full Changelog: v0.2.1...v0.3.0

v0.2.1

What's Changed

Changes

• Optimise DeepVariant

Full breakdown

• Release v0.2.1 by @leahkemp in #21
• Full Changelog: v0.2.0...v0.2.1

v0.2.0

What's Changed

New features

• Transition from calculating depth with samtools depth to mosdepth
• Add WhatsHap stats
• Add pb-CpG-tools

Other changes

• Filter out RefCall variants in DeepVariant SNP/indel vcf file
• Significantly simplify code by removing publish rules
• Remove multiple pipeface_settings.txt files for simplicity
• Add more walltime to SNV VEP
• Minor fixes/changes to documentation

Full breakdown

• Release v0.2.0 by @leahkemp in #19
• Full Changelog: v0.1.2...v0.2.0