Added nf-test for bedtools/intersect (#6658)

* migrate bedtools/intersect to nftest * changed test file paths --------- Co-authored-by: Simon Pearce <[email protected]>
nf-core · Sep 18, 2024 · 749d72f · 749d72f
1 parent 6453bce
commit 749d72f
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diff --git a/modules/nf-core/bedtools/intersect/tests/main.nf.test b/modules/nf-core/bedtools/intersect/tests/main.nf.test
@@ -0,0 +1,90 @@
+nextflow_process {
+
+    name "Test Process BEDTOOLS_INTERSECT"
+    script "../main.nf"
+    process "BEDTOOLS_INTERSECT"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bedtools"
+    tag "bedtools/intersect"
+
+    test("sarscov2 - bed - bed") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test2.bed', checkIfExists: true)
+                ]
+
+                input[1] = [[:], []]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam - bam") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/baits.bed', checkIfExists: true)
+                ]
+
+                input[1] = [[:], []]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bed - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test2.bed', checkIfExists: true)
+                ]
+
+                input[1] = [[:], []]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/bedtools/intersect/tests/main.nf.test.snap b/modules/nf-core/bedtools/intersect/tests/main.nf.test.snap
@@ -0,0 +1,101 @@
+{
+    "sarscov2 - bam - bam": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_out.bam:md5,738324efe2b1e442ceb6539a630c3fe6"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,42ba439339672f4a9193f0f0fe7a7f64"
+                ],
+                "intersect": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_out.bam:md5,738324efe2b1e442ceb6539a630c3fe6"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,42ba439339672f4a9193f0f0fe7a7f64"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-17T20:55:57.454847668"
+    },
+    "sarscov2 - bed - bed": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_out.bed:md5,afcbf01c2f2013aad71dbe8e34f2c15c"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,42ba439339672f4a9193f0f0fe7a7f64"
+                ],
+                "intersect": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_out.bed:md5,afcbf01c2f2013aad71dbe8e34f2c15c"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,42ba439339672f4a9193f0f0fe7a7f64"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-17T20:55:49.072132931"
+    },
+    "sarscov2 - bed - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_out.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,42ba439339672f4a9193f0f0fe7a7f64"
+                ],
+                "intersect": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_out.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,42ba439339672f4a9193f0f0fe7a7f64"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-17T20:56:06.259192552"
+    }
+}
diff --git a/modules/nf-core/bedtools/intersect/tests/nextflow.config b/modules/nf-core/bedtools/intersect/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: BEDTOOLS_INTERSECT {
+        ext.prefix = { "${meta.id}_out" }
+    }
+}
diff --git a/modules/nf-core/bedtools/intersect/tests/tags.yml b/modules/nf-core/bedtools/intersect/tests/tags.yml
@@ -0,0 +1,2 @@
+bedtools/intersect:
+  - "modules/nf-core/bedtools/intersect/**"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -40,9 +40,6 @@ bbmap/align:
 bcftools/convert:
   - modules/nf-core/bcftools/convert/**
   - tests/modules/nf-core/bcftools/convert/**
-bedtools/intersect:
-  - modules/nf-core/bedtools/intersect/**
-  - tests/modules/nf-core/bedtools/intersect/**
 bedtools/unionbedg:
   - modules/nf-core/bedtools/unionbedg/**
   - tests/modules/nf-core/bedtools/unionbedg/**

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