Added nf-test for picard/collectmultiplemetrics (#6296)

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

@@ -0,0 +1,112 @@
+
+nextflow_process {
+
+    name "Test Process PICARD_COLLECTMULTIPLEMETRICS"
+    script "../main.nf"
+    process "PICARD_COLLECTMULTIPLEMETRICS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "picard"
+    tag "picard/collectmultiplemetrics"
+
+    test("test-picard-collectmultiplemetrics") {
+
+        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'],[]]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.metrics[0][1].collect { file(it).name }.toSorted(),
+                    process.out.pdf[0][1].collect { file(it).name }.toSorted(),
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("test-picard-collectmultiplemetrics-nofasta") {
+
+        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'],[]]
+                input[2] = [[id:'genome'],[]]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.metrics[0][1].collect { file(it).name }.toSorted(),
+                    process.out.pdf[0][1].collect { file(it).name }.toSorted(),
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("test-picard-collectmultiplemetrics-cram") {
+
+        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/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.metrics[0][1].collect { file(it).name }.toSorted(),
+                    process.out.pdf[0][1].collect { file(it).name }.toSorted(),
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+
+}

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

@@ -0,0 +1,80 @@
+{
+    "test-picard-collectmultiplemetrics": {
+        "content": [
+            [
+                "test.CollectMultipleMetrics.alignment_summary_metrics",
+                "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "test.CollectMultipleMetrics.insert_size_metrics",
+                "test.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "test.CollectMultipleMetrics.quality_distribution_metrics"
+            ],
+            [
+                "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "test.CollectMultipleMetrics.insert_size_histogram.pdf",
+                "test.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "test.CollectMultipleMetrics.quality_distribution.pdf",
+                "test.CollectMultipleMetrics.read_length_histogram.pdf"
+            ],
+            [
+                "versions.yml:md5,b68b83e8dd0f9360453213acad639338"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T10:03:36.631174"
+    },
+    "test-picard-collectmultiplemetrics-cram": {
+        "content": [
+            [
+                "test.CollectMultipleMetrics.alignment_summary_metrics",
+                "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "test.CollectMultipleMetrics.insert_size_metrics",
+                "test.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "test.CollectMultipleMetrics.quality_distribution_metrics"
+            ],
+            [
+                "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "test.CollectMultipleMetrics.insert_size_histogram.pdf",
+                "test.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "test.CollectMultipleMetrics.quality_distribution.pdf",
+                "test.CollectMultipleMetrics.read_length_histogram.pdf"
+            ],
+            [
+                "versions.yml:md5,b68b83e8dd0f9360453213acad639338"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T10:04:13.955902"
+    },
+    "test-picard-collectmultiplemetrics-nofasta": {
+        "content": [
+            [
+                "test.CollectMultipleMetrics.alignment_summary_metrics",
+                "test.CollectMultipleMetrics.base_distribution_by_cycle_metrics",
+                "test.CollectMultipleMetrics.insert_size_metrics",
+                "test.CollectMultipleMetrics.quality_by_cycle_metrics",
+                "test.CollectMultipleMetrics.quality_distribution_metrics"
+            ],
+            [
+                "test.CollectMultipleMetrics.base_distribution_by_cycle.pdf",
+                "test.CollectMultipleMetrics.insert_size_histogram.pdf",
+                "test.CollectMultipleMetrics.quality_by_cycle.pdf",
+                "test.CollectMultipleMetrics.quality_distribution.pdf",
+                "test.CollectMultipleMetrics.read_length_histogram.pdf"
+            ],
+            [
+                "versions.yml:md5,b68b83e8dd0f9360453213acad639338"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T10:03:54.707587"
+    }
+}

tests/config/pytest_modules.yml

@@ -932,9 +932,6 @@ picard/cleansam:
 picard/collectinsertsizemetrics:
   - modules/nf-core/picard/collectinsertsizemetrics/**
   - tests/modules/nf-core/picard/collectinsertsizemetrics/**
-picard/collectmultiplemetrics:
-  - modules/nf-core/picard/collectmultiplemetrics/**
-  - tests/modules/nf-core/picard/collectmultiplemetrics/**
 picard/collectrnaseqmetrics:
   - modules/nf-core/picard/collectrnaseqmetrics/**
   - tests/modules/nf-core/picard/collectrnaseqmetrics/**