Merge pull request #12 from phac-nml/fixes-updates

Fixes updates

.github/workflows/build.yml

@@ -2,12 +2,12 @@ name: nf-iridanext CI
 on:
   push:
     branches:
-      - '*'
+      - "*"
     tags-ignore:
-      - '*'
+      - "*"
   pull_request:
     branches:
-      - '*'
+      - "*"
 jobs:
   build:
     name: Build nf-iridanext
@@ -34,13 +34,12 @@ jobs:
         with:
           java-version: ${{matrix.java_version}}
           architecture: x64
-          distribution: 'temurin'
+          distribution: "temurin"
 
       - name: Compile
         run: ./gradlew assemble
 
       - name: Tests
         run: ./gradlew check
         env:
-          GRADLE_OPTS: '-Dorg.gradle.daemon=false'
-
+          GRADLE_OPTS: "-Dorg.gradle.daemon=false"

CHANGELOG.md

@@ -1,17 +1,17 @@
 # Unreleased
 
-* Added support for writing JSON output file when using `-resume` in a pipeline.
-* Re-structured Nextflow config syntax for loading metadata from CSV file using `csv {}` section in config.
-* Added support for reading metadata from JSON file using `json {}` section in config.
-* Added support for flattening samples metadata with `iridanext.output.metadata.flatten=true`.
-* Added support for validation by custom JSON schema before writing final JSON output file (defaults to no validation). 
-    * Enable with `iridanext.output.validate=true` and set schema with `iridanext.output.schema=PATH`.
-    * If `iridanext.output.schema` is unset, validates against default JSON schema for IRIDA Next output data.
-* Added support for `iridanext.output.metadata.{ignore,keep,rename}` to ignore, keep, or rename metadata keys.
-* Expanded test suite.
+- Added support for writing JSON output file when using `-resume` in a pipeline.
+- Re-structured Nextflow config syntax for loading metadata from CSV file using `csv {}` section in config.
+- Added support for reading metadata from JSON file using `json {}` section in config.
+- Added support for flattening samples metadata with `iridanext.output.metadata.flatten=true`.
+- Added support for validation by custom JSON schema before writing final JSON output file (defaults to no validation).
+  - Enable with `iridanext.output.validate=true` and set schema with `iridanext.output.schema=PATH`.
+  - If `iridanext.output.schema` is unset, validates against default JSON schema for IRIDA Next output data.
+- Added support for `iridanext.output.metadata.{ignore,keep,rename}` to ignore, keep, or rename metadata keys.
+- Expanded test suite.
 
 # 0.1.0 - 2023/12/14
 
-* Initial release of plugin enabling the creation of a JSON file containing data to store within [IRIDA Next][irida-next].
+- Initial release of plugin enabling the creation of a JSON file containing data to store within [IRIDA Next][irida-next].
 
 [irida-next]: https://github.com/phac-nml/irida-next