Added nf-test for hapibd (#6575)

modules/nf-core/hapibd/main.nf

@@ -47,4 +47,25 @@ process HAPIBD {
         hapibd: \$(hap-ibd 2>&1 |head -n1 | sed 's/^hap-ibd.jar  \\[ version //; s/, /rev/; s/ \\]//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def avail_mem = 3072
+    if (!task.memory) {
+        log.info '[hapibd] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = (task.memory.mega*0.8).intValue()
+    }
+
+    """
+    touch ${prefix}.log
+    echo | gzip > ${prefix}.hbd.gz
+    echo | gzip > ${prefix}.ibd.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hapibd: \$(hap-ibd 2>&1 |head -n1 | sed 's/^hap-ibd.jar  \\[ version //; s/, /rev/; s/ \\]//')
+    END_VERSIONS
+    """
 }

modules/nf-core/hapibd/meta.yml

@@ -10,7 +10,7 @@ tools:
       homepage: "https://github.com/browning-lab/hap-ibd/blob/master/README.md"
       documentation: "https://github.com/browning-lab/hap-ibd/blob/master/README.md"
       doi: "10.1016/j.ajhg.2020.02.010"
-      licence: "['Apache-2.0']"
+      licence: ["Apache-2.0"]
 input:
   - meta:
       type: map

modules/nf-core/hapibd/tests/main.nf.test

@@ -0,0 +1,99 @@
+
+nextflow_process {
+
+    name "Test Process HAPIBD"
+    script "../main.nf"
+    process "HAPIBD"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "hapibd"
+
+    test("test-hapibd") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.truth.vcf.gz", checkIfExists: true)
+				]
+				input[1] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.map", checkIfExists: true)
+				input[2] = []
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert file(process.out.log[0][1]).text.contains('End Time') },
+                { assert snapshot(
+					file(process.out.hbd[0][1]).name, // empty
+					file(process.out.ibd[0][1]).name, // unstable
+					file(process.out.log[0][1]).name,
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+    test("test-hapibd-excludesamples") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.truth.vcf.gz", checkIfExists: true)
+				]
+				input[1] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.map", checkIfExists: true)
+				input[2] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/excludeSamples.txt", checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert file(process.out.log[0][1]).text.contains('End Time') },
+                { assert snapshot(
+					file(process.out.hbd[0][1]).name, // empty
+					file(process.out.ibd[0][1]).name, // unstable
+					file(process.out.log[0][1]).name,
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+    test("test-hapibd-excludesamples-stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.truth.vcf.gz", checkIfExists: true)
+				]
+				input[1] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.map", checkIfExists: true)
+				input[2] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/excludeSamples.txt", checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

modules/nf-core/hapibd/tests/main.nf.test.snap

@@ -0,0 +1,103 @@
+{
+    "test-hapibd": {
+        "content": [
+            "test.hbd.gz",
+            "test.ibd.gz",
+            "test.log",
+            [
+                "versions.yml:md5,27c1ec7c19884a358c01031f02604c2a"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T21:50:07.8312"
+    },
+    "test-hapibd-excludesamples": {
+        "content": [
+            "test.hbd.gz",
+            "test.ibd.gz",
+            "test.log",
+            [
+                "versions.yml:md5,27c1ec7c19884a358c01031f02604c2a"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T21:50:29.730739"
+    },
+    "test-hapibd-excludesamples-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.hbd.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.ibd.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,27c1ec7c19884a358c01031f02604c2a"
+                ],
+                "hbd": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.hbd.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "ibd": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.ibd.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,27c1ec7c19884a358c01031f02604c2a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T21:40:49.71258"
+    }
+}

tests/config/pytest_modules.yml

@@ -329,9 +329,6 @@ gunc/mergecheckm:
 gunc/run:
   - modules/nf-core/gunc/run/**
   - tests/modules/nf-core/gunc/run/**
-hapibd:
-  - modules/nf-core/hapibd/**
-  - tests/modules/nf-core/hapibd/**
 hicexplorer/hicpca:
   - modules/nf-core/hicexplorer/hicpca/**
   - tests/modules/nf-core/hicexplorer/hicpca/**