run validation pipelines in azure using github action (#85)

* run validation pipelines in azure using github action

Signed-off-by: Jorge Aguilera <[email protected]>

Author: jagedn

.github/workflows/nfazure.yml

@@ -0,0 +1,49 @@
+name: nf-azure CI
+on:
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: Build nf-nomad
+    if: "!contains(github.event.head_commit.message, '[ci skip]')"
+    runs-on: nfazure
+    timeout-minutes: 10
+    strategy:
+      fail-fast: false
+      matrix:
+        java_version: [19]
+
+    steps:
+      - name: Environment
+        run: env | sort
+
+      - name: Checkout
+        uses: actions/checkout@v1
+        with:
+          fetch-depth: 1
+          submodules: true
+
+      - name: Setup Java ${{ matrix.java_version }}
+        uses: actions/setup-java@v1
+        with:
+          java-version: ${{matrix.java_version}}
+          architecture: x64
+
+      - name: Compile
+        run: ./gradlew assemble
+
+      - name: Tests
+        run: ./gradlew check
+        env:
+          GRADLE_OPTS: '-Dorg.gradle.daemon=false'
+
+      - name: Install
+        run: ./gradlew clean unzipPlugin -x test -P version=nfazure
+        env:
+          GRADLE_OPTS: '-Dorg.gradle.daemon=false'
+
+      - name: Validate
+        run: |          
+          cd validation
+          export NOMAD_PLUGIN_VERSION=nfazure
+          ./run-all.sh --skiplocal --nfgithub

validation/run-all.sh

@@ -5,6 +5,7 @@ set -uex
 BUILD=0
 SKIPLOCAL=0
 NFAZURE=0
+NFGHACTION=0
 NFSUN=0
 NFSLEEP=0
 NFDEMO=0
@@ -13,6 +14,7 @@ NFDEMO=0
 [[ -f $HOME/.nextflow/plugins/nf-nomad-latest/ ]]  && BUILD=1
 [[ "$@" =~ '--skiplocal' ]] && SKIPLOCAL=1
 [[ "$@" =~ '--nfazure' ]] && NFAZURE=1
+[[ "$@" =~ '--nfgithub' ]] && NFGHACTION=1
 [[ "$@" =~ '--nfsun' ]] && NFSUN=1
 [[ "$@" =~ '--sleep' ]] && NFSLEEP=1
 [[ "$@" =~ '--demo' ]] && NFDEMO=1
@@ -69,6 +71,13 @@ else
   echo "skip nfazure"
 fi
 
+if [ "$NFGHACTION" == 1 ]; then
+  cd ~/integration-tests/az-nomadlab; NXF_ASSETS=/projects/assets nextflow run hello -w /projects/ -c nextflow.config
+  cd ~/integration-tests/az-nomadlab; NXF_ASSETS=/projects/assets nextflow run bactopia/bactopia -c nextflow.config -w /projects -profile test,docker --outdir /projects/bactopia/outdir --accession SRX4563634 --coverage 100 --genome_size 2800000 --datasets_cache /projects/bactopia/datasets
+else
+  echo "skip ghaction"
+fi
+
 
 #NOTE: In this use-case you need to be in the same network of sun-nomadlab server, for example using a tailscale connection
 #NOTE2: You need to have 2 secrets stored in your Nextlow: SUN_NOMADLAB_ACCESS_KEY and SUN_NOMADLAB_SECRET_KEY