Release 1.4.0

Author: bentsherman

.github/workflows/build.yml

@@ -1,6 +1,11 @@
 name: nf-ga4gh CI
 on:
   push:
+    branches:
+      - 'master'
+  pull_request:
+    types: [opened, reopened, synchronize]
+  workflow_dispatch:
 
 jobs:
   build:
@@ -12,7 +17,7 @@ jobs:
       fail-fast: false
       matrix:
         java_version: [
-          17, 
+          17,
           21,
         ]
 
@@ -31,13 +36,10 @@ jobs:
         with:
           java-version: ${{matrix.java_version}}
           distribution: 'temurin'
-          cache: 'gradle'                
-
-      - name: Compile
-        run: ./gradlew assemble
+          cache: 'gradle'
 
-      - name: Tests
-        run: ./gradlew check
+      - name: Unit tests
+        run: make test
         env:
           GRADLE_OPTS: '-Dorg.gradle.daemon=false'
 
@@ -71,15 +73,15 @@ jobs:
           distribution: 'temurin'
           cache: 'gradle'
 
-      - name: Install Plugin
-        run: |
-          make install
-
       - name: Install Nextflow ${{ matrix.nextflow_version }}
         uses: nf-core/setup-nextflow@v2
         with:
           version: ${{ matrix.nextflow_version }}
 
+      - name: Install Plugin
+        run: |
+          make install
+
       - name: Install TES Server
         run: |
           # https://github.com/ohsu-comp-bio/funnel/releases/tag/v0.11.8
@@ -92,19 +94,16 @@ jobs:
       - name: Get plugin version
         shell: bash
         run: |
-          PLUGIN_VERSION="$(./gradlew -q properties | awk -F': ' '/^version:/ {print $2; exit}')"
+          PLUGIN_VERSION="$(cat VERSION)"
           echo "PLUGIN_VERSION=${PLUGIN_VERSION}" >> "$GITHUB_ENV"
           echo "Using plugin version: ${PLUGIN_VERSION}"
 
       - name: Install nf-canary
         run: |
-          cd ..
-          git clone https://github.com/seqeralabs/nf-canary
-          cd nf-canary
-          cat <<EOF > nextflow.config.tes
+          cat <<EOF > nextflow.config
           // Nextflow config file for running on TES Backend
           plugins {
-            id "nf-ga4gh@${PLUGIN_VERSION}"
+            id 'nf-ga4gh@${PLUGIN_VERSION}'
           }
           process {
               executor = 'tes'
@@ -116,23 +115,20 @@ jobs:
               basicUsername              = null
               basicPassword              = null
           }
+          report.enabled = true
+          timeline.enabled = true
           EOF
 
       - name: Run nf-canary
         run: |
-          cd ../nf-canary
           export NXF_ANSI_LOG=false
-          nextflow run main.nf \
-            -config nextflow.config.tes \
-            -with-report report.html \
-            -with-timeline timeline.html
+          nextflow run seqeralabs/nf-canary
 
       - name: Stage Reports
         if: always()
         run: |
           mkdir -p $GITHUB_WORKSPACE/results
-          cd ../nf-canary
-          
+
           # Nextflow Logs
           cp -f report.html timeline.html .nextflow.log $GITHUB_WORKSPACE/results/ || true
 

VERSION

@@ -0,0 +1 @@
+1.4.0

build.gradle

@@ -1,16 +1,9 @@
-// Plugins
 plugins {
-    // https://github.com/nextflow-io/nextflow-plugin-gradle/tree/v1.0.0-beta.14
     id 'io.nextflow.nextflow-plugin' version '1.0.0-beta.14'
 }
 
-// Dependencies
 dependencies {
-    compileOnly "io.nextflow:nextflow:25.10.4"
-    compileOnly "org.apache.groovy:groovy:4.0.21"
-    compileOnly "org.pf4j:pf4j:3.10.0"
-    compileOnly "org.slf4j:slf4j-api:2.0.7"
-
+    // required by the auto-generated TES Java SDK
     api "com.google.code.gson:gson:2.11.0"
     api "com.squareup.okhttp:logging-interceptor:2.7.5"
     api "com.squareup.okhttp:okhttp:2.7.5"
@@ -20,16 +13,12 @@ dependencies {
     api "org.threeten:threetenbp:1.3.5"
 }
 
-// Plugin version
-version = '1.3.1'
+version = project.file('VERSION').text.trim()
 
-// Nextflow plugin configuration
 nextflowPlugin {
-    // Minimum Nextflow version
-    nextflowVersion = '25.10.4'
+    nextflowVersion = '25.10.0'
 
-    // Plugin metadata
-    provider = 'nextflow-io'
+    provider = 'nextflow'
     className = 'nextflow.ga4gh.Ga4ghPlugin'
     extensionPoints = [
         'nextflow.ga4gh.tes.executor.TesExecutor'