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Fixes updates #12

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merged 3 commits into from
Jan 19, 2024
Merged

Fixes updates #12

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7b05dea
Switched config of metadata control to be under samples
apetkau Jan 19, 2024
a655a89
Updated docs
apetkau Jan 19, 2024
bc3ecdb
Ran prettier
apetkau Jan 19, 2024
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11 changes: 5 additions & 6 deletions .github/workflows/build.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,12 +2,12 @@ name: nf-iridanext CI
on:
push:
branches:
- '*'
- "*"
tags-ignore:
- '*'
- "*"
pull_request:
branches:
- '*'
- "*"
jobs:
build:
name: Build nf-iridanext
Expand All @@ -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"
20 changes: 10 additions & 10 deletions CHANGELOG.md
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@@ -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
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