Merge pull request #26 from microbiomedata/25-ci-wdl-validation

CI WDL validation on ReadbasedAnalysis.wdl

.github/workflows/wdl_linter.yml

@@ -0,0 +1,27 @@
+name: MiniWDL linter CI
+
+on:
+  pull_request:
+    branches: master
+
+jobs:
+  run-miniwdl:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.8' # specify the Python version you need
+
+    - name: Install MiniWDL
+      run: |
+        python -m pip install --upgrade pip
+        pip install miniwdl
+    - name: Run MiniWDL
+      run: |
+        # Add the commands to run your MiniWDL workflow
+        miniwdl check --suppress UnknownRuntimeKey ReadbasedAnalysis.wdl

ReadbasedAnalysis.wdl

@@ -61,14 +61,12 @@ workflow ReadbasedAnalysis {
             enabled_tools_gottcha2 = enabled_tools_gottcha2,
             enabled_tools_kraken2 = enabled_tools_kraken2,
             enabled_tools_centrifuge = enabled_tools_centrifuge, 
-            docker = docker,
             db_gottcha2 = db_gottcha2,
             db_kraken2 = db_kraken2,
             db_centrifuge = db_centrifuge,
             docker = docker,
             gottcha2_info = profilerGottcha2.info,
             gottcha2_report_tsv = profilerGottcha2.report_tsv,
-            gottcha2_info = profilerGottcha2.info,
             centrifuge_report_tsv = profilerCentrifuge.report_tsv,
             centrifuge_info = profilerCentrifuge.info,
             kraken2_report_tsv = profilerKraken2.report_tsv,

version.txt

@@ -1 +1 @@
-v1.0.7
+v1.0.8