Added nf-test for gatk/unifiedgenotyper (#6322)

nf-core · Aug 26, 2024 · aeaa1d7 · aeaa1d7
1 parent 821fa4c
commit aeaa1d7
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Showing 6 changed files with 71 additions and 45 deletions.
diff --git a/modules/nf-core/gatk/unifiedgenotyper/tests/main.nf.test b/modules/nf-core/gatk/unifiedgenotyper/tests/main.nf.test
@@ -0,0 +1,56 @@
+
+nextflow_process {
+
+    name "Test Process GATK_UNIFIEDGENOTYPER"
+    script "../main.nf"
+    process "GATK_UNIFIEDGENOTYPER"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gatk"
+    tag "gatk/unifiedgenotyper"
+
+    test("test-gatk-unifiedgenotyper") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test' ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+				]
+				input[1] = [
+				    [id: 'test'],
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+				]
+				input[2] = [
+				    [id: 'test'],
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+				]
+				input[3] = [
+				    [id: 'test'],
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)
+				]
+				input[4] = [[],[]]
+                input[5] = [[],[]]
+                input[6] = [[],[]]
+                input[7] = [[],[]]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					path(process.out.vcf[0][1]).vcf.variantsMD5,
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/gatk/unifiedgenotyper/tests/main.nf.test.snap b/modules/nf-core/gatk/unifiedgenotyper/tests/main.nf.test.snap
@@ -0,0 +1,15 @@
+{
+    "test-gatk-unifiedgenotyper": {
+        "content": [
+            "577c77d9323f6256931a6846eaac3f40",
+            [
+                "versions.yml:md5,f0dfc5a0252a665c12a2b27444f73e67"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T13:30:01.119639"
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -389,9 +389,6 @@ gappa/examineheattree:
 gatk/indelrealigner:
   - modules/nf-core/gatk/indelrealigner/**
   - tests/modules/nf-core/gatk/indelrealigner/**
-gatk/unifiedgenotyper:
-  - modules/nf-core/gatk/unifiedgenotyper/**
-  - tests/modules/nf-core/gatk/unifiedgenotyper/**
 gatk4/calibratedragstrmodel:
   - modules/nf-core/gatk4/calibratedragstrmodel/**
   - tests/modules/nf-core/gatk4/calibratedragstrmodel/**

diff --git a/tests/modules/nf-core/gatk/unifiedgenotyper/main.nf b/tests/modules/nf-core/gatk/unifiedgenotyper/main.nf
diff --git a/tests/modules/nf-core/gatk/unifiedgenotyper/nextflow.config b/tests/modules/nf-core/gatk/unifiedgenotyper/nextflow.config
diff --git a/tests/modules/nf-core/gatk/unifiedgenotyper/test.yml b/tests/modules/nf-core/gatk/unifiedgenotyper/test.yml