Releases: leahkemp/pipeface
Releases · leahkemp/pipeface
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
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Full Changelog: v0.6.2...v0.7.0
Contributors
EddieLF, jimmykhchiu, and 4 other contributors
Assets 2
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
-
Full Changelog: v0.6.0...v0.6.1
Contributors
leahkemp
Assets 2
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
Contributors
kisarur and leahkemp
Assets 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
Contributors
leahkemp
Assets 2
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
Contributors
leahkemp
Assets 2
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
Contributors
leahkemp