v0.10.2

What's Changed

Bug fixes

• Address LongTR bug that appears on some samples. Fixes: #92

Other changes

• Use fun new GPU queue

Full breakdown

• • Release 0.10.2 by @leahkemp in #94

• Full Changelog: v0.10.1...v0.10.2

v0.10.1

What's Changed

Bug fixes

• Fix access to LongTR install in pipeface:0.0.2 container Fixes #89 (thanks to Kirat Alreja @kiratalreja3 for reporting!)

Full breakdown

• Release 0.10.1 by @leahkemp in #91

• Full Changelog: v0.10.0...v0.10.1

v0.10.0

What's Changed

New features

• Add longTR tandem repeat calling

Other changes

• Add documentation on getting CADD SV database
• Drop reporting of pipeface version in docs/software_versions.txt file since I keep forgetting to update it
  Resolve warning message related to matching of input tuple for split_multiallele process (doesn't cause an error or affect pipeline outputs)

Full breakdown

• Release 0.10.0 by @leahkemp in #88

• Full Changelog: v0.9.4...v0.10.0

v0.9.4

What's Changed

Bug fixes

• Fix grouping by family ID. Fixes #85

Full breakdown

• Release 0.9.4 by @leahkemp in #86

• Full Changelog: v0.9.3...v0.9.4

v0.9.3

What's Changed

Other changes

• Make pipeface portable and more modular as a by product (thanks to Gavin Monahan @gavinmonahan for feedback regarding pipeline modularity and allowing me access to pawsey for testing + initial scoping out of this feature!). Also thanks to Kisaru Liyanage @kisarur and Matthew Downton for feedback and testing in preparation for supporting pipeface on workflow-catalogue!)

Full breakdown

• Release 0.9.3 by @leahkemp in #83

• Full Changelog: v0.9.2...v0.9.3

v0.9.2

What's Changed

Bug fixes

• Fix trio processes not run. Fixes #76

Other changes:

• Improvements to the VEP annotation
  • Intergenic or intronic consequences are prioritised over upstream/downstream variants. As well as higher-impact consequences such as missense, splice variants and frameshift (thanks to investigation by Andre Reis @almreis!)
• Add extra error checks. Fixes #78
• Add some minor, nonetheless un-mentioned software dependencies
• Minor updates to documentation

Full breakdown

• Release 0.9.2 by @leahkemp in #81

• Full Changelog: v0.9.1...v0.9.2

v0.9.1

What's Changed

Bug fixes

• Drop ref filling for now. Fixes #73

Full breakdown

• Release 0.9.1 by @leahkemp in #74

• Full Changelog: v0.9.0...v0.9.1

v0.9.0

What's Changed

New features

• Add duo analysis

Other changes

• Simplify code where possible (then make it more complicated while adding duo analysis :) )
  • Code formatting
  • Drop the un-needed scrape_bam_header proccess (thanks to the feedback from Arthur Gymer @awgymer!)
  • Use groovy to call the haploid aware clair3/deepvariant code
  • Consolidate error messages
  • Properly handle loading of bam index (.bai file) when the in data format is an aligned BAM, should help with pipeline portability (thanks to the feedback from Arthur Gymer @awgymer!)
• Speed up mosdepth by dropping writing of per base file
• Include all variants in annotated VCF irrespective of their VEP support
• Reference filling for joint SV VCF's (thanks to feedback from Rocio Rius!)
• Drop pb-CpG-tools and use minimod for base modification analysis for both ont and pacbio data
• Include header in minimod BED output files
• Seperate unphased base modifications into their own minimod output file (no longer included in combined file)
• Update documentation
• Increase default process resources where needed to account for more dataset types/sizes

Full breakdown

• Release 0.9.0 by @leahkemp in #72
• Full Changelog: v0.8.0...v0.9.0

v0.8.0

What's Changed

New features

• Add somalier

Other changes

• DeepVariant/DeepTrio Update (version 1.6.1 to version 1.8.0) thanks to @kisarur !. This means even more speed increases and in turn cost reductions!
• Tag pipeface version in pipeface_settings.txt files (thanks to the feedback from Edward Formaini @EddieLF !)
• Update samtools, htslib, minimod, bcftools
• Add un-reported bedtools in the software_versions.txt file
• Organising of nextflow_pipeface.config file

Full breakdown

• Release 0.8.0 by @leahkemp in #62

• Full Changelog: v0.7.0...v0.8.0

v0.7.0

What's Changed

New features

• Haploid aware mode thanks to Kirat Alreja @kiratalreja3 !
• Output SNP/indel GVCF files for greater flexibility with downstream population analyses

Other changes

• Use environmental modules for mosdepth and pb-CpG-tools instead of requiring the user to define their binaries in parameters_pipeface.json
• Add zero genotypes in jasmine as default (thanks to the feedback from Jimmy Chiu @jimmykhchiu !)
• Drop gnomad/clinvar SV annotation (thanks to the feedback from Andre Reis @almreis !)
• Add platform specific settings for jasmine (thanks to the feedback from Andre Reis @almreis !)
• Tag sample ID in the read group info in bam headers during minimap. In turn this removes the need to tag bams with this information in the DeepTrio step, which will help reduce the size of the work directory in cohort mode (thanks to feedback from Edward Formaini @EddieLF !)
• Improvements to documentation
• Improvements to code formatting
• Improvement to user input error checks (thanks to the feedback from Monique Dunstan @moniquedunstan !)

Full breakdown

• Release 0.7.0 by @leahkemp and @kiratalreja3 in #58

• Full Changelog: v0.6.2...v0.7.0