Added nf-test for metabat2/jgisummarizebamcontigdepths

modules/nf-core/metabat2/jgisummarizebamcontigdepths/environment.yml

@@ -2,6 +2,5 @@ name: metabat2_jgisummarizebamcontigdepths
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::metabat2=2.15

modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf

@@ -35,4 +35,15 @@ process METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS {
         metabat2: \$( metabat2 --help 2>&1 | head -n 2 | tail -n 1| sed 's/.*\\:\\([0-9]*\\.[0-9]*\\).*/\\1/' )
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo | gzip > ${prefix}.txt.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        metabat2: \$( metabat2 --help 2>&1 | head -n 2 | tail -n 1| sed 's/.*\\:\\([0-9]*\\.[0-9]*\\).*/\\1/' )
+    END_VERSIONS
+    """
 }

modules/nf-core/metabat2/jgisummarizebamcontigdepths/tests/main.nf.test

@@ -0,0 +1,60 @@
+
+nextflow_process {
+
+    name "Test Process METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS"
+    script "../main.nf"
+    process "METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "metabat2"
+    tag "metabat2/jgisummarizebamcontigdepths"
+
+    test("test-metabat2-jgisummarizebamcontigdepths") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-metabat2-jgisummarizebamcontigdepths-stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

modules/nf-core/metabat2/jgisummarizebamcontigdepths/tests/main.nf.test.snap

@@ -0,0 +1,68 @@
+{
+    "test-metabat2-jgisummarizebamcontigdepths": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.txt.gz:md5,c7448ff92b336561540717e7b0ca0702"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,2884d72385b65d0737899da5cb9e89d5"
+                ],
+                "depth": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.txt.gz:md5,c7448ff92b336561540717e7b0ca0702"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,2884d72385b65d0737899da5cb9e89d5"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T20:02:46.985235"
+    },
+    "test-metabat2-jgisummarizebamcontigdepths-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,2884d72385b65d0737899da5cb9e89d5"
+                ],
+                "depth": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,2884d72385b65d0737899da5cb9e89d5"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T20:01:24.531629"
+    }
+}

tests/config/pytest_modules.yml

@@ -422,9 +422,6 @@ merquryfk/katgc:
 merquryfk/ploidyplot:
   - modules/nf-core/merquryfk/ploidyplot/**
   - tests/modules/nf-core/merquryfk/ploidyplot/**
-metabat2/jgisummarizebamcontigdepths:
-  - modules/nf-core/metabat2/jgisummarizebamcontigdepths/**
-  - tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/**
 metabat2/metabat2:
   - modules/nf-core/metabat2/metabat2/**
   - tests/modules/nf-core/metabat2/metabat2/**