Added nf-test for cnvkit/call (#6582)

* Added nf-test for cnvkit/call * Removed defaults
nf-core · Sep 5, 2024 · bf39676 · bf39676
1 parent 50b3cbc
commit bf39676
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Showing 8 changed files with 201 additions and 55 deletions.
diff --git a/modules/nf-core/cnvkit/call/environment.yml b/modules/nf-core/cnvkit/call/environment.yml
@@ -2,6 +2,5 @@ name: cnvkit_call
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::cnvkit=0.9.10
diff --git a/modules/nf-core/cnvkit/call/main.nf b/modules/nf-core/cnvkit/call/main.nf
@@ -33,4 +33,15 @@ process CNVKIT_CALL {
         cnvkit: \$(cnvkit.py version | sed -e 's/cnvkit v//g')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.cns
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cnvkit: \$(cnvkit.py version | sed -e 's/cnvkit v//g')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/cnvkit/call/tests/main.nf.test b/modules/nf-core/cnvkit/call/tests/main.nf.test
@@ -0,0 +1,83 @@
+
+nextflow_process {
+
+    name "Test Process CNVKIT_CALL"
+    script "../main.nf"
+    process "CNVKIT_CALL"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "cnvkit"
+    tag "cnvkit/call"
+
+    test("test-cnvkit-call") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file('https://raw.githubusercontent.com/etal/cnvkit/v0.9.9/test/formats/amplicon.cns', checkIfExists: true),
+				    []
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-cnvkit-call-with-vcf") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file('https://raw.githubusercontent.com/etal/cnvkit/v0.9.9/test/formats/amplicon.cns', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-cnvkit-call-with-vcf-stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file('https://raw.githubusercontent.com/etal/cnvkit/v0.9.9/test/formats/amplicon.cns', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/cnvkit/call/tests/main.nf.test.snap b/modules/nf-core/cnvkit/call/tests/main.nf.test.snap
@@ -0,0 +1,107 @@
+{
+    "test-cnvkit-call": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.cns:md5,7746029caf9ecc134a075a2d50be269f"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,f47253e21b991f72a741d6b5c9a351a5"
+                ],
+                "cns": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.cns:md5,7746029caf9ecc134a075a2d50be269f"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f47253e21b991f72a741d6b5c9a351a5"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T22:24:41.048386"
+    },
+    "test-cnvkit-call-with-vcf": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.cns:md5,2a4b3da8a8131a4ed4ae902a9f96a405"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,f47253e21b991f72a741d6b5c9a351a5"
+                ],
+                "cns": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.cns:md5,2a4b3da8a8131a4ed4ae902a9f96a405"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f47253e21b991f72a741d6b5c9a351a5"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T22:24:50.134984"
+    },
+    "test-cnvkit-call-with-vcf-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.cns:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,f47253e21b991f72a741d6b5c9a351a5"
+                ],
+                "cns": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.cns:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f47253e21b991f72a741d6b5c9a351a5"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T22:24:56.743954"
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -94,9 +94,6 @@ circexplorer2/parse:
 clippy:
   - modules/nf-core/clippy/**
   - tests/modules/nf-core/clippy/**
-cnvkit/call:
-  - modules/nf-core/cnvkit/call/**
-  - tests/modules/nf-core/cnvkit/call/**
 cnvkit/export:
   - modules/nf-core/cnvkit/export/**
   - tests/modules/nf-core/cnvkit/export/**

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