port gatk4/calculatecontamination to nf-test (#5603)

* port to nf-test update stub * prettier * prettier * add assertion for segmentation
nf-core · May 15, 2024 · 77ffba9 · 77ffba9
1 parent 7d81481
commit 77ffba9
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diff --git a/modules/nf-core/gatk4/calculatecontamination/main.nf b/modules/nf-core/gatk4/calculatecontamination/main.nf
@@ -43,4 +43,16 @@ process GATK4_CALCULATECONTAMINATION {
         gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    prefix   = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.contamination.table
+    touch ${prefix}.segmentation.table
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test b/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test
@@ -0,0 +1,106 @@
+nextflow_process {
+
+    name "Test Process GATK4_CALCULATECONTAMINATION"
+    script "../main.nf"
+    process "GATK4_CALCULATECONTAMINATION"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gatk4"
+    tag "gatk4/calculatecontamination"
+
+    test("human - pileup-table") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test2.pileups.table', checkIfExists: true),
+                    [] ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match("versions") },
+                { assert snapshot(file(process.out.contamination.get(0).get(1)).readLines()[0]).match() }
+            )
+        }
+
+    }
+
+    test("human - pileup-table - matched-pair") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test2.pileups.table', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.pileups.table', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match("versions_pair") },
+                { assert snapshot(file(process.out.contamination.get(0).get(1)).readLines()[0]).match() }
+            )
+        }
+
+    }
+
+    test("human - pileup-table - segmentation") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test2.pileups.table', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.pileups.table', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match("versions_segmentation") },
+                { assert snapshot(file(process.out.contamination.get(0).get(1)).readLines()[0]).match("contamination") },
+                { assert snapshot(file(process.out.segmentation.get(0).get(1)).readLines()[0]).match("segmentation") }
+            )
+        }
+
+    }
+
+    test("human - pileup-table - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test2.pileups.table', checkIfExists: true),
+                    [] ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test.snap b/modules/nf-core/gatk4/calculatecontamination/tests/main.nf.test.snap
@@ -0,0 +1,127 @@
+{
+    "versions_pair": {
+        "content": [
+            [
+                "versions.yml:md5,4a72b1da18f7045d470225881e7266a6"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-05-15T11:08:17.057861"
+    },
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,4a72b1da18f7045d470225881e7266a6"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-05-15T11:08:07.193762"
+    },
+    "versions_segmentation": {
+        "content": [
+            [
+                "versions.yml:md5,4a72b1da18f7045d470225881e7266a6"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-05-15T11:08:26.99069"
+    },
+    "segmentation": {
+        "content": [
+            "#<METADATA>SAMPLE=tumour"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-05-15T12:57:38.845287"
+    },
+    "human - pileup-table": {
+        "content": [
+            "sample\tcontamination\terror"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-05-15T11:09:16.292509"
+    },
+    "human - pileup-table - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.contamination.table:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.segmentation.table:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,4a72b1da18f7045d470225881e7266a6"
+                ],
+                "contamination": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.contamination.table:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "segmentation": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.segmentation.table:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,4a72b1da18f7045d470225881e7266a6"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-05-15T12:56:14.817045"
+    },
+    "human - pileup-table - matched-pair": {
+        "content": [
+            "sample\tcontamination\terror"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-05-15T11:09:26.408848"
+    },
+    "contamination": {
+        "content": [
+            "sample\tcontamination\terror"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.0"
+        },
+        "timestamp": "2024-05-15T12:57:38.840651"
+    }
+}
diff --git a/modules/nf-core/gatk4/calculatecontamination/tests/nextflow.config b/modules/nf-core/gatk4/calculatecontamination/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: GATK4_CALCULATECONTAMINATION {
+        ext.args = { "--tumor-segmentation ${meta.id}.segmentation.table" }
+    }
+}
diff --git a/modules/nf-core/gatk4/calculatecontamination/tests/tags.yml b/modules/nf-core/gatk4/calculatecontamination/tests/tags.yml
@@ -0,0 +1,2 @@
+gatk4/calculatecontamination:
+  - "modules/nf-core/gatk4/calculatecontamination/**"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -585,9 +585,6 @@ gatk/unifiedgenotyper:
 gatk4/applyvqsr:
   - modules/nf-core/gatk4/applyvqsr/**
   - tests/modules/nf-core/gatk4/applyvqsr/**
-gatk4/calculatecontamination:
-  - modules/nf-core/gatk4/calculatecontamination/**
-  - tests/modules/nf-core/gatk4/calculatecontamination/**
 gatk4/calibratedragstrmodel:
   - modules/nf-core/gatk4/calibratedragstrmodel/**
   - tests/modules/nf-core/gatk4/calibratedragstrmodel/**

diff --git a/tests/modules/nf-core/gatk4/calculatecontamination/main.nf b/tests/modules/nf-core/gatk4/calculatecontamination/main.nf
diff --git a/tests/modules/nf-core/gatk4/calculatecontamination/nextflow.config b/tests/modules/nf-core/gatk4/calculatecontamination/nextflow.config
diff --git a/tests/modules/nf-core/gatk4/calculatecontamination/test.yml b/tests/modules/nf-core/gatk4/calculatecontamination/test.yml
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		gatk4/calculatecontamination:
		- "modules/nf-core/gatk4/calculatecontamination/**"