Carrot setup

.carrot/carrot_eval.wdl

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+version 1.0
+
+task compare {
+    input {
+        String result
+        String image_to_use
+    }
+    command {
+        echo "Checking the result from previous test:"
+        echo "~{result}"
+    }
+    runtime {
+        docker: image_to_use
+    }
+    output {
+        File comparison_result = stdout()
+    }
+}
+
+workflow eval_workflow {
+    input {
+        String result
+        String image_to_use
+    }
+    call compare {
+        input:
+            result = result,
+            image_to_use = image_to_use
+    }
+    output {
+        File comparison_result = compare.comparison_result
+    }
+}

.carrot/carrot_test.wdl

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+version 1.0
+
+task test_htsjdk {
+    input {
+        File input_file
+        String image_to_use
+    }
+    command {
+        echo "pretending to run test on ~{input_file}"
+    }
+    runtime {
+        docker: image_to_use
+    }
+
+    output {
+        String result = stdout()
+    }
+}
+
+workflow test_workflow {
+    input {
+        File input_file
+        String image_to_use
+    }
+    call test_htsjdk {
+        input:
+            input_file = input_file,
+            image_to_use = image_to_use
+    }
+    output {
+        String result = test_htsjdk.result
+    }
+}
+
+

.carrot/eval.json

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+{
+  "eval_workflow.result": "test_output:test_workflow.result"
+}
+

.carrot/eval_defaults.json

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+{
+  "eval_workflow.image_to_use": "ubuntu:latest"
+}
+

.carrot/run_test.sh

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+python3.10 -m carrot_cli test run --test_input test.json --eval_input eval.json 36d33423-15a5-4d8b-aa5d-cb04eb6f6017

.carrot/test.json

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+{
+  "test_workflow.image_to_use": "ubuntu:latest"
+}
+

.carrot/test_defaults.json

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+{
+  "test_workflow.input_file": "gs://hellbender/test/resources/nio/big.txt"
+}

.carrot/update_wdls.sh

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+python3.10 -m carrot_cli template update 03ff49e8-40ee-411e-b16f-f43b377cb6e9 --test_wdl carrot_test.wdl --eval_wdl carrot_eval.wdl

.github/workflows/carrot_run_test_from_pr_comment.yml

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+name: carrot-test-run-from-pr-comment
+on:
+  issue_comment:
+    types: [created]
+jobs:
+  publish-test:
+    runs-on: ubuntu-18.04
+    steps:
+      - name: Parse comment
+        uses: broadinstitute/[email protected]
+        with:
+          software-name: gatk
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          topic-name: ${{ secrets.CARROT_TOPIC_NAME }}
+          sa-key: ${{ secrets.CARROT_SA_KEY }}
+          minimum-permissions: write

Dockerfile

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+# This docker build is here to enable Carrot tests
+# It's not intended for any other purpose
+FROM eclipse-temurin:17
+
+COPY . .
+RUN ./gradlew compileTestJava
+ENTRYPOINT bash