Swap clippy to nf-test (nf-core#7277)

fellen31 · Jan 10, 2025 · 5b0eb56 · 5b0eb56
1 parent 1254968
commit 5b0eb56
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Showing 8 changed files with 286 additions and 70 deletions.
diff --git a/modules/nf-core/clippy/main.nf b/modules/nf-core/clippy/main.nf
@@ -37,4 +37,18 @@ process CLIPPY {
         clippy: \$(clippy -v)
     END_VERSIONS
     """
+
+    stub:
+    prefix   = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_Peaks.bed
+    touch ${prefix}_Summits.bed
+    touch ${prefix}_intergenic_regions.gtf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        clippy: \$(clippy -v)
+    END_VERSIONS
+    """
+
 }
diff --git a/modules/nf-core/clippy/tests/main.nf.test b/modules/nf-core/clippy/tests/main.nf.test
@@ -0,0 +1,90 @@
+nextflow_process {
+
+    name "Test Process CLIPPY"
+    script "../main.nf"
+    process "CLIPPY"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "clippy"
+
+    test("non-intergenic") {
+
+        config "./nextflow.config"
+
+        when {
+            params {
+                module_args = '-inter 3'
+            }
+            process {
+                """
+                input[0] = [
+                    [  id:'test' ], // meta map
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/clipseq/crosslinks/clippy.bed", checkIfExists: true)
+                ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/chr21_gencode.gtf', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("intergenic") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [  id:'test' ], // meta map
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/clipseq/crosslinks/clippy.bed", checkIfExists: true)
+                ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/chr21_gencode.gtf', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("non-intergenic - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [  id:'test' ], // meta map
+                    []
+                ]
+                input[1] = []
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/clippy/tests/main.nf.test.snap b/modules/nf-core/clippy/tests/main.nf.test.snap
@@ -0,0 +1,177 @@
+{
+    "non-intergenic - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_Peaks.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_Summits.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_intergenic_regions.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,b9f94c70bed994e77aa7feccaa25aff5"
+                ],
+                "intergenic_gtf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_intergenic_regions.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "peaks": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_Peaks.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "summits": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_Summits.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b9f94c70bed994e77aa7feccaa25aff5"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-08T16:59:22.78408481"
+    },
+    "non-intergenic": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_rollmean10_minHeightAdjust1.0_minPromAdjust1.0_minGeneCount5_Peaks.bed:md5,d793b0bafe5478207bfe80dd635a215c"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_rollmean10_minHeightAdjust1.0_minPromAdjust1.0_minGeneCount5_Summits.bed:md5,afc2143816a8ae91329d7e557a91eeba"
+                    ]
+                ],
+                "2": [
+
+                ],
+                "3": [
+                    "versions.yml:md5,b9f94c70bed994e77aa7feccaa25aff5"
+                ],
+                "intergenic_gtf": [
+
+                ],
+                "peaks": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_rollmean10_minHeightAdjust1.0_minPromAdjust1.0_minGeneCount5_Peaks.bed:md5,d793b0bafe5478207bfe80dd635a215c"
+                    ]
+                ],
+                "summits": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_rollmean10_minHeightAdjust1.0_minPromAdjust1.0_minGeneCount5_Summits.bed:md5,afc2143816a8ae91329d7e557a91eeba"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b9f94c70bed994e77aa7feccaa25aff5"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-08T16:58:19.283343973"
+    },
+    "intergenic": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_rollmean10_minHeightAdjust1.0_minPromAdjust1.0_minGeneCount5_Peaks.bed:md5,d793b0bafe5478207bfe80dd635a215c"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_rollmean10_minHeightAdjust1.0_minPromAdjust1.0_minGeneCount5_Summits.bed:md5,afc2143816a8ae91329d7e557a91eeba"
+                    ]
+                ],
+                "2": [
+
+                ],
+                "3": [
+                    "versions.yml:md5,b9f94c70bed994e77aa7feccaa25aff5"
+                ],
+                "intergenic_gtf": [
+
+                ],
+                "peaks": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_rollmean10_minHeightAdjust1.0_minPromAdjust1.0_minGeneCount5_Peaks.bed:md5,d793b0bafe5478207bfe80dd635a215c"
+                    ]
+                ],
+                "summits": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_rollmean10_minHeightAdjust1.0_minPromAdjust1.0_minGeneCount5_Summits.bed:md5,afc2143816a8ae91329d7e557a91eeba"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b9f94c70bed994e77aa7feccaa25aff5"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-08T16:59:13.088102108"
+    }
+}
diff --git a/modules/nf-core/clippy/tests/nextflow.config b/modules/nf-core/clippy/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'CLIPPY_INTERGENIC' {
+        ext.args = params.module_args
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -76,9 +76,6 @@ cellrangeratac/mkfastq:
 cellrangeratac/mkref:
   - modules/nf-core/cellrangeratac/mkref/**
   - tests/modules/nf-core/cellrangeratac/mkref/**
-clippy:
-  - modules/nf-core/clippy/**
-  - tests/modules/nf-core/clippy/**
 cnvnator/cnvnator:
   - modules/nf-core/cnvnator/cnvnator/**
   - tests/modules/nf-core/cnvnator/cnvnator/**

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