Prepare for version 1.0.2

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

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'
 }