Added nf-test for picard/collectwgsmetrics

modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test

@@ -0,0 +1,83 @@
+
+nextflow_process {
+
+    name "Test Process PICARD_COLLECTWGSMETRICS"
+    script "../main.nf"
+    process "PICARD_COLLECTWGSMETRICS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "picard"
+    tag "picard/collectwgsmetrics"
+
+    test("test-picard-collectwgsmetrics") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // 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:'genome'],
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+				]
+				input[2] = [
+				    [id:'genome'],
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+				]
+				input[3] = []
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.metrics[0][1]).text.contains('coverage	high_quality_coverage_count'),
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("test-picard-collectwgsmetrics-with-interval") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+				    []
+				]
+				input[1] = [
+				    [id:'genome'],
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+				]
+				input[2] = [
+				    [id:'genome'],
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+				]
+				input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/picard/baits.interval_list', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.metrics[0][1]).text.contains('coverage	high_quality_coverage_count'),
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+}

modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap

@@ -0,0 +1,28 @@
+{
+    "test-picard-collectwgsmetrics-with-interval": {
+        "content": [
+            true,
+            [
+                "versions.yml:md5,06b5898fb06823b736c90e1dcebe75fe"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T11:02:46.301176"
+    },
+    "test-picard-collectwgsmetrics": {
+        "content": [
+            true,
+            [
+                "versions.yml:md5,06b5898fb06823b736c90e1dcebe75fe"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T11:02:25.132069"
+    }
+}

tests/config/pytest_modules.yml

@@ -1097,9 +1097,6 @@ picard/collectmultiplemetrics:
 picard/collectrnaseqmetrics:
   - modules/nf-core/picard/collectrnaseqmetrics/**
   - tests/modules/nf-core/picard/collectrnaseqmetrics/**
-picard/collectwgsmetrics:
-  - modules/nf-core/picard/collectwgsmetrics/**
-  - tests/modules/nf-core/picard/collectwgsmetrics/**
 picard/fastqtosam:
   - modules/nf-core/picard/fastqtosam/**
   - tests/modules/nf-core/picard/fastqtosam/**