METABAT2_METABAT2: Add nf-test and stub (#7196)

* Add stub * Add nf-test (empty TSV for depth test expected) * Update modules/nf-core/metabat2/metabat2/tests/main.nf.test * Apply suggestions from code review * Use name for expected empty file
nf-core · Dec 11, 2024 · 299a26f · 299a26f
1 parent 7860035
commit 299a26f
Show file tree

Hide file tree

Showing 7 changed files with 296 additions and 69 deletions.
diff --git a/modules/nf-core/metabat2/metabat2/main.nf b/modules/nf-core/metabat2/metabat2/main.nf
@@ -45,4 +45,23 @@ process METABAT2_METABAT2 {
         metabat2: \$( metabat2 --help 2>&1 | head -n 2 | tail -n 1| sed 's/.*\\:\\([0-9]*\\.[0-9]*\\).*/\\1/' )
     END_VERSIONS
     """
+
+    stub:
+    def args             = task.ext.args   ?: ''
+    def prefix           = task.ext.prefix ?: "${meta.id}"
+    def decompress_depth = depth           ? "gzip -d -f $depth"    : ""
+    def depth_file       = depth           ? "-a ${depth.baseName}" : ""
+
+    """
+    echo "" | gzip -c > ${prefix}.1.fa.gz
+    echo "" | gzip -c > ${prefix}.1.tooShort.fa.gz
+    echo "" | gzip -c > ${prefix}.1.lowDepth.fa.gz
+    echo "" | gzip -c > ${prefix}.1.unbinned.fa.gz
+    echo "" | gzip -c > ${prefix}.tsv.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        metabat2: \$( metabat2 --help 2>&1 | head -n 2 | tail -n 1| sed 's/.*\\:\\([0-9]*\\.[0-9]*\\).*/\\1/' )
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/metabat2/metabat2/tests/main.nf.test b/modules/nf-core/metabat2/metabat2/tests/main.nf.test
@@ -0,0 +1,99 @@
+// nf-core modules test metabat2/metabat2
+nextflow_process {
+
+    name "Test Process METABAT2_METABAT2"
+    script "../main.nf"
+    process "METABAT2_METABAT2"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "metabat2"
+    tag "metabat2/metabat2"
+    tag "metabat2/jgisummarizebamcontigdepths"
+
+    test("sarscov2 - genome - fasta") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [id: 'test', single_end: false],
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                                []
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - genome - fasta - depths") {
+
+        setup {
+            run("METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS") {
+                script "../../jgisummarizebamcontigdepths/main.nf"
+                process {
+                    """
+                    input[0] = [
+                                    [id: 'test', single_end: false],
+                                    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),
+                                ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = Channel
+                            .fromPath(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                            .map { it -> [[ id:'test', single_end:false ], it] }
+                            .join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.membership[0][1]).name).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - genome - fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [id: 'test', single_end: false],
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                                []
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/metabat2/metabat2/tests/main.nf.test.snap b/modules/nf-core/metabat2/metabat2/tests/main.nf.test.snap
@@ -0,0 +1,178 @@
+{
+    "sarscov2 - genome - fasta": {
+        "content": [
+            {
+                "0": [
+
+                ],
+                "1": [
+
+                ],
+                "2": [
+
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv.gz:md5,f50e2528d24fcd9a200cae3421945f05"
+                    ]
+                ],
+                "4": [
+
+                ],
+                "5": [
+                    "versions.yml:md5,872d18278c2ba7812c62a8bc6b2120eb"
+                ],
+                "fasta": [
+
+                ],
+                "lowdepth": [
+
+                ],
+                "membership": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv.gz:md5,f50e2528d24fcd9a200cae3421945f05"
+                    ]
+                ],
+                "tooshort": [
+
+                ],
+                "unbinned": [
+
+                ],
+                "versions": [
+                    "versions.yml:md5,872d18278c2ba7812c62a8bc6b2120eb"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-11T12:28:01.970872008"
+    },
+    "sarscov2 - genome - fasta - depths": {
+        "content": [
+            "test.tsv.gz"
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-11T13:08:47.777561763"
+    },
+    "sarscov2 - genome - fasta - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.1.tooShort.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.1.lowDepth.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.1.unbinned.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.1.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "5": [
+                    "versions.yml:md5,872d18278c2ba7812c62a8bc6b2120eb"
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.1.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "lowdepth": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.1.lowDepth.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "membership": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "tooshort": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.1.tooShort.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "unbinned": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.1.unbinned.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,872d18278c2ba7812c62a8bc6b2120eb"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-11T12:28:32.122007408"
+    }
+}
diff --git a/...nf-core/metabat2/metabat2/nextflow.config → ...e/metabat2/metabat2/tests/nextflow.config b/...nf-core/metabat2/metabat2/nextflow.config → ...e/metabat2/metabat2/tests/nextflow.config
@@ -1,9 +1,5 @@
 process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
     withName: METABAT2_METABAT2 {
         ext.args = '--minContig 1500 --minCV 0.1 --minCVSum 0.1 --minClsSize 10 --minS 2'
     }
-
 }
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -338,9 +338,6 @@ merquryfk/katgc:
 merquryfk/ploidyplot:
   - modules/nf-core/merquryfk/ploidyplot/**
   - tests/modules/nf-core/merquryfk/ploidyplot/**
-metabat2/metabat2:
-  - modules/nf-core/metabat2/metabat2/**
-  - tests/modules/nf-core/metabat2/metabat2/**
 metaeuk/easypredict:
   - modules/nf-core/metaeuk/easypredict/**
   - tests/modules/nf-core/metaeuk/easypredict/**

diff --git a/tests/modules/nf-core/metabat2/metabat2/main.nf b/tests/modules/nf-core/metabat2/metabat2/main.nf
diff --git a/tests/modules/nf-core/metabat2/metabat2/test.yml b/tests/modules/nf-core/metabat2/metabat2/test.yml