Added nf-test stub for gatk4/variantfiltration (#5676)

* Added nf-test stub for gatk4/variantfiltration * Update for lint * Update for lint
nf-core · May 22, 2024 · 0040936 · 0040936
1 parent 63d6994
commit 0040936
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diff --git a/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test b/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test
@@ -0,0 +1,87 @@
+nextflow_process {
+
+    name "Test Process GATK4_VARIANTFILTRATION"
+    script "../main.nf"
+    process "GATK4_VARIANTFILTRATION"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gatk4"
+    tag "gatk4/variantfiltration"
+
+    test("test_gatk4_variantfiltration_vcf_input") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'genome' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id:'genome' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ]
+                input[3] = [
+                    [ id:'genome' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions,
+                                  file(process.out.vcf.get(0).get(1)).name,
+                                  file(process.out.tbi.get(0).get(1)).name).match() },
+            )
+        }
+
+    }
+
+    test("test_gatk4_variantfiltration_gz_input") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'genome' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id:'genome' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ]
+                input[3] = [
+                    [ id:'genome' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions,
+                                  file(process.out.vcf.get(0).get(1)).name,
+                                  file(process.out.tbi.get(0).get(1)).name).match() },
+            )
+        }
+
+    }
+
+}
+
diff --git a/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test.snap b/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test.snap
@@ -0,0 +1,30 @@
+{
+    "test_gatk4_variantfiltration_gz_input": {
+        "content": [
+            [
+                "versions.yml:md5,96943659275ba62de1f0d283a2f6e97b"
+            ],
+            "test.vcf.gz",
+            "test.vcf.gz.tbi"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.2"
+        },
+        "timestamp": "2024-05-22T22:43:27.609784"
+    },
+    "test_gatk4_variantfiltration_vcf_input": {
+        "content": [
+            [
+                "versions.yml:md5,96943659275ba62de1f0d283a2f6e97b"
+            ],
+            "test.vcf.gz",
+            "test.vcf.gz.tbi"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.2"
+        },
+        "timestamp": "2024-05-22T22:42:55.316294"
+    }
+}
diff --git a/modules/nf-core/gatk4/variantfiltration/tests/tags.yml b/modules/nf-core/gatk4/variantfiltration/tests/tags.yml
@@ -0,0 +1,2 @@
+gatk4/variantfiltration:
+  - "modules/nf-core/gatk4/variantfiltration/**"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -653,9 +653,6 @@ gatk4/splitcram:
 gatk4/splitintervals:
   - modules/nf-core/gatk4/splitintervals/**
   - tests/modules/nf-core/gatk4/splitintervals/**
-gatk4/variantfiltration:
-  - modules/nf-core/gatk4/variantfiltration/**
-  - tests/modules/nf-core/gatk4/variantfiltration/**
 gatk4/variantrecalibrator:
   - modules/nf-core/gatk4/variantrecalibrator/**
   - tests/modules/nf-core/gatk4/variantrecalibrator/**

diff --git a/tests/modules/nf-core/gatk4/variantfiltration/main.nf b/tests/modules/nf-core/gatk4/variantfiltration/main.nf
diff --git a/tests/modules/nf-core/gatk4/variantfiltration/nextflow.config b/tests/modules/nf-core/gatk4/variantfiltration/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/variantfiltration/test.yml b/tests/modules/nf-core/gatk4/variantfiltration/test.yml