Add long-running integration tests runnable by Azure DevOps

src/TriggerService.Tests/TriggerService.Tests.csproj

@@ -15,6 +15,7 @@
   </ItemGroup>
 
   <ItemGroup>
+    <PackageReference Include="Azure.Identity" Version="1.9.0" />
     <PackageReference Include="Microsoft.Azure.Batch" Version="15.4.0" />
     <PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.5.0" />
     <PackageReference Include="Moq" Version="4.18.4" />

src/TriggerService.Tests/test-wdls/mutect2/mutect2.inputs.json

@@ -0,0 +1,32 @@
+{
+  "Mutect2.gatk_docker": "broadinstitute/gatk:latest",
+
+  "Mutect2.intervals": "/datasettestinputs/dataset/references/hg19/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.baits.interval_list",
+  "Mutect2.scatter_count": 50,
+  "Mutect2.m2_extra_args": "--downsampling-stride 20 --max-reads-per-alignment-start 6 --max-suspicious-reads-per-alignment-start 6",
+  "Mutect2.filter_funcotations": "True",
+  "Mutect2.funco_reference_version": "hg19",
+  "Mutect2.funco_data_sources_tar_gz": "/datasettestinputs/dataset/gatk4-somatic-snvs-indels/funcotator/funcotator_dataSources.v1.6.20190124s.tar.gz",
+  "Mutect2.funco_transcript_selection_list": "/datasettestinputs/dataset/gatk4-somatic-snvs-indels/funcotator/transcriptList.exact_uniprot_matches.AKT1_CRLF2_FGFR1.txt",
+  "Mutect2.max_retries": 3,
+
+  "Mutect2.ref_fasta": "/datasettestinputs/dataset/references/hg19/Homo_sapiens_assembly19.fasta",
+  "Mutect2.ref_dict": "/datasettestinputs/dataset/references/hg19/Homo_sapiens_assembly19.dict",
+  "Mutect2.ref_fai": "/datasettestinputs/dataset/references/hg19/Homo_sapiens_assembly19.fasta.fai",
+  "Mutect2.normal_reads": "/datasettestinputs/dataset/gatk4-somatic-snvs-indels/HCC1143/HCC1143_normal.bam",
+  "Mutect2.normal_reads_index": "/datasettestinputs/dataset/gatk4-somatic-snvs-indels/HCC1143/HCC1143_normal.bai",
+  "Mutect2.tumor_reads": "/datasettestinputs/dataset/gatk4-somatic-snvs-indels/HCC1143/HCC1143.bam",
+  "Mutect2.tumor_reads_index": "/datasettestinputs/dataset/gatk4-somatic-snvs-indels/HCC1143/HCC1143.bai",
+
+  "Mutect2.pon": "/datasettestinputs/dataset/gatk4-somatic-snvs-indels/Mutect2-exome-panel.vcf",
+  "Mutect2.pon_idx": "/datasettestinputs/dataset/gatk4-somatic-snvs-indels/Mutect2-exome-panel.vcf.idx",
+  "Mutect2.gnomad": "/datasettestinputs/dataset/gatk4-somatic-snvs-indels/af-only-gnomad.raw.sites.vcf",
+  "Mutect2.gnomad_idx": "/datasettestinputs/dataset/gatk4-somatic-snvs-indels/af-only-gnomad.raw.sites.vcf.idx",
+  "Mutect2.variants_for_contamination": "/datasettestinputs/dataset/gatk4-somatic-snvs-indels/small_exac_common_3.vcf",
+  "Mutect2.variants_for_contamination_idx": "/datasettestinputs/dataset/gatk4-somatic-snvs-indels/small_exac_common_3.vcf.idx",
+  "Mutect2.realignment_index_bundle": "/datasettestinputs/dataset/gatk4-somatic-snvs-indels/Homo_sapiens_assembly38.index_bundle",
+
+  "Mutect2.emergency_extra_disk": 20
+}
+
+

src/TriggerService.Tests/test-wdls/mutect2/mutect2.trigger.json

@@ -0,0 +1,6 @@
+{
+  "WorkflowUrl": "https://raw.githubusercontent.com/microsoft/gatk4-somatic-snvs-indels-azure/az2.7.0/mutect2.wdl",
+  "WorkflowInputsUrl": "https://raw.githubusercontent.com/microsoft/CromwellOnAzure/main/long-running-int-test/src/TriggerService.Tests/test-wdls/mutect2/mutect2.inputs.json",
+  "WorkflowOptionsUrl": null,
+  "WorkflowDependenciesUrl": null
+}

src/deploy-cromwell-on-azure/Deployer.cs

@@ -2108,12 +2108,19 @@ private static async Task<bool> IsWorkflowSuccessfulAfterLongPollingAsync(IStora
             {
                 try
                 {
-                    var succeeded = container.GetBlobs(prefix: $"succeeded/{id}").Count() == 1;
-                    var failed = container.GetBlobs(prefix: $"failed/{id}").Count() == 1;
+                    var hasSucceeded = container.GetBlobs(prefix: $"succeeded/{id}").Count() == 1;
+                    var failedWorkflowTriggerFileBlobs = container.GetBlobs(prefix: $"failed/{id}").ToList();
+                    var hasFailed = failedWorkflowTriggerFileBlobs.Count == 1;
 
-                    if (succeeded || failed)
+                    if (hasSucceeded || hasFailed)
                     {
-                        return succeeded && !failed;
+                        if (hasFailed)
+                        {
+                            var failedContent = (await container.GetBlobClient(failedWorkflowTriggerFileBlobs.First().Name).DownloadContentAsync()).Value.Content.ToString();
+                            ConsoleEx.WriteLine($"Failed workflow trigger JSON: {failedContent}");
+                        }
+
+                        return hasSucceeded && !hasFailed;
                     }
                 }
                 catch (Exception exc)