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CHANGELOG.md

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Changelog

All notable changes to the pipeline-name pipeline.

The format is based on Keep a Changelog.

This project adheres to Semantic Versioning.

[Unreleased]

Added

  • Add GRIDSS2 assembly
  • Add GRIDSS2 preprocessing
  • Add supported Nextflow version to README.md
  • Add PlantUML diagram

Changed

  • Update PlantUML action to v1.0.1
  • Update memory allocations in M64.config

[6.1.0] - 2024-03-12

Removed

  • Local versions of modularized functions

Added

  • CODEOWNERS file

[6.0.0] - 2024-02-23

Changed

  • Perform additional pipeline runs towards release v6.0.0

[6.0.0-rc.2] - 2024-02-06

Added

  • Add NFTest

Changed

  • Update DELLY v1.1.3 to v1.2.6
  • Update submodules

Removed

  • Remove set_env method code in default/methods.config

[6.0.0-rc.1] - 2023-08-02

Added

  • YAML input

Changed

  • Update to latest commit of `pipeline-Nextflow-config``
  • Update pipeline SVG
  • Update YAML input and tests in README.md
  • Update PipeVal to v4.0.0-rc.2
  • Parse sample ID from tumor BAM for output directory naming
  • Update README.md to clarify adjustable parameters and note lab default values

Removed

  • CSV input

[5.0.0] - 2023-01-27

Changed

  • Update README.md for release 5.0.0
  • Perform additional test to release 5.0.0

[5.0.0-rc.1] - 2023-01-24

Changed

  • Update README.md for release 5.0.0-rc.1
  • Move param checking to methods.config using schema.config
  • Parameterize Docker registry
  • Use ghcr.io/uclahs-cds as default registry
  • Simplify output directory declaration for each process using addParams and use output_dir_base

Added

  • Add PipeVal:v3.0.0 using pipeline-Nextflow-module to validate the input CSV file
  • Parameter algorithm to select the SV caller(s) of choice in template.config
  • Add Manta SV caller

Removed

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

[4.0.0] - 2022-10-13

Added

  • Retry mechanism to retry a process with higher memory - PR #69

Changed

  • Standardize the variable names in the pipeline and change input CSV column names from control_sample_bam to normal_bam and tumor_sample_bam to tumor_bam
  • Standardize output filename using generate_standardized_filename
  • Upgrade Delly 1.0.3 to 1.1.3

[3.0.0] - 2022-07-25

Added

  • Add F16.config to enable F16 node compatibility

Changed

  • Rename call-sSV.nf to main.nf and replace mainScript with name in main.nf line 15
  • Upgrade BCTools 1.12 to 1.15.1
  • Remove save_intermediate_files argument in default.config as it is already specified in template.config
  • Standardize the repo structure based on NF pipeline template
  • Update README.md with resource locations and runtime of Delly v1.0.3 on different datasets and node types
  • Change Delly version from 0.9.1 to 1.0.3 in default.config

Fixed

  • Fix memory allocation for process 'query_SampleName_BCFtools' in F2.config - Discussion #28 and PR #33
  • Fix F2 detection in methods.config - PR #32

[2.0.0] - 2022-02-17

Added

  • Add the process "filter_BCF_BCFtools" to filter Non-Pass calls.

[1.0.1] - 2021-12-09

Changed

  • Change Delly version from 0.8.7 to 0.9.1 in nextflow.config and metadata.yaml
  • Use sha512sum to replace 'python -m validate -t sha512-gen'

[1.0.0] - 2021-10-29

Changed

  • Minor changes of wording in CHANGELOG.md and metadata.yaml

[1.0.0-rc1] - 2021-10-18

Added

  • Use Delly to call the somatic structural variants (SVs) of one tumor sample and a matched control sample, further filter the somatic SVs.
  • Add option to specify map_qual, min_clique_size, and mad_cutoff Delly filters to reduce the runtime.
  • Use BCFtools to automatically generate the samples.tsv that is needed by the sSV filtering (see https://github.com/dellytools/delly).