Release 5.3.0

Automatically generated after merging #187.

What's Changed

• Bump external/pipeline-Nextflow-module from 537da32 to 1cfa9fa in the pipeline-submodules group by @dependabot in #167
• Add release management workflows by @nwiltsie in #171
• Bump uclahs-cds/tool-PlantUML-action from 1.0.1 to 1 (alias) by @dependabot in #172
• Update cluster reference paths by @nwiltsie in #173
• Add nextflow.config to release management process by @nwiltsie in #174
• Bump the pipeline-submodules group across 1 directory with 2 updates by @dependabot in #179
• Add resource handler by @Faizal-Eeman in #178
• Bump the pipeline-submodules group with 2 updates by @dependabot in #181
• Add BCF2VCF workflow by @Faizal-Eeman in #184
• Add CIRCOS plot by @Faizal-Eeman in #186
• Prepare for version 5.3.0 by @boutros-lab-infrastructure-owner in #187

New Contributors

• @boutros-lab-infrastructure-owner made their first contribution in #187

Full Changelog: v5.2.0...v5.3.0

v5.2.0

Updates include but not limited to,

• Optimized CPU allocation for Manta gSV calling
• base_resource_update available for users to update CPU/memory allocations if required

v5.1.0

Updates include but not limited to,

• Use HG003 as test sample for NFTest

v5.0.0

Updates include but not limited to,

• DELLY updated to v1.2.6
• Memory allocations optimized
• NFTest added
• PlantUML based pipeline diagram

Other updates and standardizations are listed in CHANGELOG.md

v5.0.0-rc.1

Added

• Add parameter validation
• Add YAML input
• Sample ID parsing from input BAM

Removed

• Remove params GSV and GCNV from template.config
• Remove CSV input

Changed

• Output filename standardizations

v4.0.1

Patch release that include

• PipeVal v3.0.0 udpate
• Dockerhub to GH registry migration

v4.0.0

Merge PR #72 to main.

Major updates include but not limited to,

• Delly upgraded to 1.13
• BCFtools upgraded to 1.15.1
• F16 compatibility

v4.0.0-rc.1

Merge PR #57 to main.

Added

• Add the Issue Report template
• Add the Pull Request template
• Add GPL 2.0

Fixed

• Fix Issue #55: fix F2 detection
• Fix Issue #32: remove option '--exclude' in delly cnv
• Fix Issue #33: should pass the mappability_map file instead of the exclusion file to regenotype_gCNV_Delly

Changed

• Change the input file schema by removing variant_type,reference_fasta,reference_fasta_index, put them into template.config.
• Change partition types from lowmem/midmem/execute to F2/F32/F72/M64.
• Standardize the output structure.
• Standardize the configuration structure.

call-gSV Manta and Regenotyping additions

Added

• Added ability to call germline SVs with Manta
• Added parameters to control which SV caller is used (run_delly & run_manta)
• Added pipeline version from manifest to pipeline logging output
• Added CNV VCF outputs to QC processes
• Added two new processes to regenotype SVs or CNVs with Delly (regenotype_gSV_Delly & regenotype_gCNV_Delly)
• Added parameters and input mode to control which type of regenotyping is run (mode, run_regenotyping & run_discovery)

Changed

• Changed output directories to correspond with tool name casing

call-gSV Docker Updates

Changed

• Updated modules to point to tool specific Docker Hub repos
• Update of BCFtools from 1.11 to 1.12
• Update of RTG-tools from 3.11 to 3.12