Glimpse tests

broadinstitute · Aug 6, 2024 · a345bd4 · a345bd4
1 parent 145e94b
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diff --git a/test/Glimpse2Imputation/test_inputs.json b/test/Glimpse2Imputation/test_inputs.json
@@ -0,0 +1,9 @@
+{
+    "Glimpse2Imputation.output_basename":"test",
+    "Glimpse2Imputation.ref_dict":"gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+    "Glimpse2Imputation.reference_chunks":"gs://palantir-workflows-test-data/Glimpse2Imputation/two_chunk_reference_panel.txt",
+    "Glimpse2Imputation.sample_ids":["hg002","hg005"],
+    "Glimpse2Imputation.cpu_ligate":1,
+    "Glimpse2Imputation.mem_gb_phase":6,
+    "Glimpse2Imputation.crams":["gs://palantir-workflows-test-data/Glimpse2Imputation/hg002_1x.bam","gs://palantir-workflows-test-data/Glimpse2Imputation/hg005_1x.bam"]
+}
diff --git a/test/Glimpse2Imputation/test_outputs.json b/test/Glimpse2Imputation/test_outputs.json
@@ -0,0 +1,8 @@
+{
+    "Glimpse2Imputation.coverage_metrics":"gs://palantir-workflows-test-data/Glimpse2Imputation/phase_output_stats_coverage.txt.gz",
+    "Glimpse2Imputation.qc_metrics":"gs://palantir-workflows-test-data/Glimpse2Imputation/test.qc_metrics.tsv",
+    "Glimpse2Imputation.imputed_vcf_index":"gs://palantir-workflows-test-data/Glimpse2Imputation/test.imputed.vcf.gz.tbi",
+    "Glimpse2Imputation.glimpse_ligate_monitoring":null,
+    "Glimpse2Imputation.glimpse_phase_monitoring":null,
+    "Glimpse2Imputation.imputed_vcf":null
+}
diff --git a/test/watt_config.yml b/test/watt_config.yml
@@ -24,3 +24,10 @@ CompareBenchmarks:
     base:
       test_inputs: "/test/CompareBenchmarks/test_base_inputs.json"
       expected_outputs: "/test/CompareBenchmarks/test_base_outputs.json"
+
+Glimpse2Imputation:
+  path: "/GlimpseImputationPipeline/Glimpse2Imputation.wdl"
+  tests:
+    base:
+      test_inputs: "/test/Glimpse2Imputation/test_inputs.json"
+      expected_outputs: "/test/Glimpse2Imputation/test_outputs.json"