diff --git a/CHANGELOG.md b/CHANGELOG.md index 12dca8e..599135d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,38 +1,38 @@ # Changelog + All notable changes to the pipeline-recalibrate-BAM pipeline. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/). This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). ---- - -## [Unreleased] +## [1.0.2] - 2024-10-08 ### Added - Add release management workflows from `tool-create-release` -### [Changed] +### Changed + - Use `run_validate_PipeVal_with_metadata` to gate on validation - Move index/dictionary file discovery to configuration stage - Include all parameters from `default.config` in the README ---- - ## [1.0.1] - 2024-05-29 -### [Changed] +### Changed + - Update Nextflow configuration test workflows - Use `methods.setup_process_afterscript()` for process logs -### [Fixed] -- Resolve interval path for original given intervals to ensure the index file for intervals is found when present +### Fixed ---- +- Resolve interval path for original given intervals to ensure the index file for intervals is found when present ## [1.0.0] - 2024-03-13 -### [Added] + +### Added + - Sort BAMs before merging for consistent order of output BAM @PG header lines - Add NFTest case - Add new flow diagram to README @@ -43,33 +43,34 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm - Add Nextflow configuration test action and two regression tests - Add requirements to README -### [Changed] +### Changed + - Use modularized `set_env` function - Use modularized `check_limits` function ---- - ## [1.0.0-rc.4] - 2023-09-29 -### [Fixed] + +### Fixed + - Resource updater to allow update for all processes - Channel handling to save contamintion estimate files ---- - ## [1.0.0-rc.3] - 2023-08-09 -### [Added] -- Customization options for which input BAMs to delete with metapipeline ---- +### Added + +- Customization options for which input BAMs to delete with metapipeline ## [1.0.0-rc.2] - 2023-08-02 -### [Added] -- Custom resource allocation updates through configuration parameters ---- +### Added + +- Custom resource allocation updates through configuration parameters ## [1.0.0-rc.1] - 2023-07-27 -### [Added] + +### Added + - Basic configuration setup - Input YAML templates and handling - Per-patient input YAML handling @@ -82,3 +83,11 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm - Intermediate file deletion - Schema validation - Documentation + +[1.0.0]: /~https://github.com/uclahs-cds/pipeline-recalibrate-BAM/compare/v1.0.0-rc.4...v1.0.0 +[1.0.0-rc.1]: /~https://github.com/uclahs-cds/pipeline-recalibrate-BAM/releases/tag/v1.0.0-rc.1 +[1.0.0-rc.2]: /~https://github.com/uclahs-cds/pipeline-recalibrate-BAM/compare/v1.0.0-rc.1...v1.0.0-rc.2 +[1.0.0-rc.3]: /~https://github.com/uclahs-cds/pipeline-recalibrate-BAM/compare/v1.0.0-rc.2...v1.0.0-rc.3 +[1.0.0-rc.4]: /~https://github.com/uclahs-cds/pipeline-recalibrate-BAM/compare/v1.0.0-rc.3...v1.0.0-rc.4 +[1.0.1]: /~https://github.com/uclahs-cds/pipeline-recalibrate-BAM/compare/v1.0.0...v1.0.1 +[1.0.2]: /~https://github.com/uclahs-cds/pipeline-recalibrate-BAM/compare/v1.0.1...v1.0.2 diff --git a/nextflow.config b/nextflow.config index bbbc619..372fd8f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -3,5 +3,5 @@ manifest { name = 'recalibrate-BAM' author = 'Yash Patel, Nicholas Wiltsie' description = 'Nextflow pipeline to perform Indel Realignment and Base Quality Score Recalibration' - version = '1.0.1' + version = '1.0.2' }