Releases: leahkemp/pipeface
Releases · leahkemp/pipeface
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:
- 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 v0.4.0 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
Assets 2
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
Contributors
leahkemp
Assets 2
v0.1.2
What's Changed
New features
- SNP/indel annotation (hg38 only)
Bug fixes
Other changes
- Implement deepvariant directly (ie. remove the parabricks layer)
- Tag snp/indel caller, sv caller and mapper/phaser in filename at publish and remove some semi-duplicate rules
- Remove un-needed output files (gvcf file and sniffles snf file)
- Convert from programmatically reporting software versions to reporting software versions (and now variant database versions) in a single file in the documentation. Each version of pipeface will report the exact software/database versions used in the pipeline, assuming the default nextflow_pipeface.config file is used.
- Addition of the description of the niche pipeface fills
- Credit to collaborators
- Fixing the rendering of new lines in the mermaid diagrams
- More walltime for minimap2 and clair3
- Other minor changes to documentation
Full breakdown
- Release v0.1.2 by @leahkemp in #13
- Full Changelog: v0.1.1...v0.1.2
Contributors
leahkemp
Assets 2
v0.1.1
What's Changed
Overview
- Extend checks on user input's for in_data.csv file
- Lighten the disk usage of minimap2 by removing the need for the samtools addreplacerg step
- Increase the walltime for the merge_runs process
- Fix bug in reported SV caller when a single SV caller is selected
- Minor changes to code comments
Full breakdown
- Release v0.1.1 by @leahkemp in #6
- Full Changelog: v0.1.0...v0.1.1
Contributors
leahkemp
Assets 2
v0.1.0 - first release!
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