Add testcase for missing readgroup

genepi · May 29, 2024 · 72ce241 · 72ce241
1 parent e9ac0b4
commit 72ce241
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Showing 3 changed files with 40 additions and 1 deletion.
diff --git a/tests/data/bam/HG002.bam b/tests/data/bam/HG002.bam
diff --git a/tests/mitocalling.nf.test b/tests/mitocalling.nf.test
@@ -47,7 +47,7 @@ nextflow_pipeline {
         when {
             params {
                project = "test-job"
-               files = "$projectDir/tests/data/bam/*.bam"
+               files = "$projectDir/tests/data/bam/HG00096*.bam"
                mode = "mutect2"
                output = "out"
                output_reports = "reports"
@@ -155,4 +155,28 @@ nextflow_pipeline {
 
     }
 
+    test("Run sample without readgroup an mutect2") {
+
+        setup {
+            DownloadUtil.downloadAndExtractZip("https://mitoverse.i-med.ac.at/downloads/6-samples.zip", "${launchDir}/input")
+        }
+
+        when {
+            params {
+               project = "test-job"
+               files = "$projectDir/tests/data/bam/HG002.bam"
+               mode = "mutect2"
+               output = "out"
+               output_reports = "reports"
+               output_auxiliary = "files"
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert snapshot(path("${launchDir}/out/variants.annotated.txt"),workflow.trace).match()
+        }
+
+    }
+
 }
diff --git a/tests/mitocalling.nf.test.snap b/tests/mitocalling.nf.test.snap
@@ -74,6 +74,21 @@
         },
         "timestamp": "2024-03-07T23:06:50.681516749"
     },
+    "Run sample without readgroup an mutect2": {
+        "content": [
+            "variants.annotated.txt:md5,0fea21d7e7fc9881a2c959f1ca0c0923",
+            {
+                "tasksFailed": 0,
+                "tasksCount": 10,
+                "tasksSucceeded": 10
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0-rc1",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-29T12:04:01.840857"
+    },
     "Runs with 6 samples provided as testdata with mutserve": {
         "content": [
             "variants.annotated.txt:md5,4f06be3759a04ff20fa189dd9f5d2685",