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CHANGELOG.md

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Changelog

All notable changes to the call-gSV pipeline.

[Unreleased]

[5.2.0] - 2024-07-03

Added

  • Add methods.modify_base_allocations() to update resource allocation

Changed

  • Use methods.setup_process_afterscript() for process logs
  • Increase CPU allocation for Manta

[5.1.0] - 2024-06-10

Changed

  • Use HG003 as test sample for NFTest
  • Update Nextflow configuration test workflows

[5.0.0] - 2024-03-15

Added

  • Add PlantUML diagram
  • Add configtest-F16 for nextflow pipeline test
  • Add processes to node configs
  • Call methods.setup_docker_cpus() in config/methods.config
  • CODEOWNERS file
  • Add NFTest for gSV discovery
  • Add workflow to create release bundles with submodules
  • Add workflow to render PlantUML images to SVG
  • Add workflow to build and deploy documentation to GitHub Pages
  • Add workflow to run Nextflow configuration regression tests
  • Add one regression test

Changed

  • Update version in render-puml action
  • Add exit code 1 to Manta retry strategy
  • Set up process retry mechanism
  • Parameterize tool output dirs in main.nf
  • Parameterize workflow log dir in main.nf
  • Update DELLY v1.1.3 to v1.2.6

Removed

  • methods.set_docker_sudo() from config/methods.config
  • Remove set_env method code in config/methods.config
  • Local copies of resource allocation functions

[5.0.0-rc.1] - 2023-10-30

Changed

  • Standardize DELLY output filenames
  • Enable save_intermediate_files in bcftools.nf and rtgtools.nf
  • Standardize Manta output filenames
  • Use strings gSV and gCNV as list for param variant_type in template.config
  • Update README to reflect YAML support
  • Parse sample ID from input BAM for output directory naming

Added

  • Add schema for parameter validation
  • Add YAML input

Removed

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

[4.0.1] - 2022-12-12

Changed

  • Parameterize Docker registry
  • Use ghcr.io/uclahs-cds as default registry

Added

  • Add PipeVal using pipeline-Nextflow-module to validate the input CSV file

Removed

  • Remove module/validation.nf as PipeVal sub-module is used

[4.0.0] - 2022-08-17

Added

  • Add F16.config to allow F16 compatibility for the pipeline

Changed

  • Update README.md for 4.0.0
  • Move save_intermediate_files from default.config to template.config and set it to false
  • Update BCFtools 1.12 to 1.15.1
  • Update Delly 1.0.3 to 1.1.3
  • Update Delly 0.9.1 to 1.0.3
  • Standardize repo structure and rename the NF script name from call-gSV.nf to main.nf

[4.0.0-rc.1] - 2022-07-29

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.

[3.0.0] - 2021-07-01

Added

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

Changed

  • Change output directories to correspond with tool name casing

[2.2.0] - 2021-05-07

Changed

  • Update 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

[2.1.0] - 2021-04-01

Added

  • Add Validate-nf logging outputs to output logging directory

Changed

  • Update Validate-nf tool version from 1.0.0 to 2.1.0 (Resolves issue #18)

[2.0.0] - 2021-03-30

Added

  • Implement of Delly CNV, with output file conversions and SHA512s
  • Add mappability map to config inputs

Changed

  • Update Delly dockerfile to use bl-base
  • Include a tag of "SV" or "CNV" in output files, as appropriate

[1.0.1] - 2021-03-04

Changed

  • Change Docker run permissions (docker.sudo and docker.runOptions)
  • Fix issue #9

[1.0.0] - 2021-03-01

Added

  • Initial call-gSV pipeline release