ADD argnorm module

nf-core · Jul 2, 2024 · 02c4b6d · 02c4b6d
1 parent 95d5284
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diff --git a/modules/nf-core/argnorm/environment.yml b/modules/nf-core/argnorm/environment.yml
@@ -0,0 +1,7 @@
+name: "argnorm"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::argnorm=0.5.0"
diff --git a/modules/nf-core/argnorm/main.nf b/modules/nf-core/argnorm/main.nf
@@ -0,0 +1,40 @@
+process ARGNORM {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/argnorm:0.5.0--pyhdfd78af_0':
+        'biocontainers/argnorm:0.5.0--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(input_tsv)
+    val(db)
+    val(hamronized)
+    val(tool)
+
+    output:
+    tuple val(meta), path("*.tsv"), emit: tsv
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '0.5.0'
+    """
+    argnorm \\
+        $tool \\
+        -i $input_tsv \\
+        -o $prefix \\
+        --db $db \\
+        $hamronized
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        argnorm: $VERSION
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/argnorm/meta.yml b/modules/nf-core/argnorm/meta.yml
@@ -0,0 +1,65 @@
+name: "argnorm"
+description: Normalize antibiotic resistance genes (ARGs) using the ARO ontology (developed by CARD).
+keywords:
+  - amr
+  - antimicrobial resistance
+  - arg
+  - antimicrobial resistance genes
+  - genomics
+  - metagenomics
+  - normalization
+  - drug categorization
+tools:
+  - "argnorm":
+      description: "Normalize antibiotic resistance genes (ARGs) using the ARO ontology (developed by CARD)."
+      homepage: "https://argnorm.readthedocs.io/en/latest/"
+      documentation: "https://argnorm.readthedocs.io/en/latest/"
+      tool_dev_url: "https://github.com/BigDataBiology/argNorm"
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - input_tsv:
+      type: file
+      description: ARG annotation output
+      pattern: "*.tsv"
+
+  - db:
+      type: string
+      description: Database used for ARG annotation
+      pattern: "sarg|ncbi|resfinder|deeparg|megares|argannot|resfinderfg"
+
+  - hamronized:
+      type: string
+      description: Indicate ARG annotation output has been processed by hAMRonization
+      pattern: "|--hamronized"
+
+  - tool:
+      type: string
+      description: ARG annotation tool used
+      pattern: "argsoap|abricate|deeparg|resfinder|amrfinderplus"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - tsv:
+      type: file
+      description: Normalized argNorm output
+      pattern: "*.tsv"
+
+authors:
+  - "@Vedanth-Ramji"
+maintainers:
+  - "@Vedanth-Ramji"
diff --git a/modules/nf-core/argnorm/tests/main.nf.test b/modules/nf-core/argnorm/tests/main.nf.test
@@ -0,0 +1,108 @@
+nextflow_process {
+    name "Test Process ARGNORM"
+    script "../main.nf"
+    process "ARGNORM"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "argnorm"
+
+    test("argnorm - amrfinderplus_ncbi_raw - tsv") {
+        when {
+            process {
+                """                
+                input[0] = [
+                    [ id:'test.tsv', single_end:false ], // meta map                                                                                                                           
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/amrfinderplus/test_output.tsv", checkIfExists: true)                              
+                ]
+                input[1] = 'ncbi'
+                input[2] = 'amrfinderplus'
+                input[3] = ''
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("argnorm - amrfinderplus_ncbi_hamronized - tsv") {
+        when {
+            process {
+                """                
+                input[0] = [
+                    [ id:'test.tsv', single_end:false ], // meta map                                                                                                                           
+                    file("https://raw.githubusercontent.com/BigDataBiology/argNorm/main/examples/hamronized/amrfinderplus.ncbi.orfs.tsv", checkIfExists: true)                              
+                ]
+                input[1] = 'ncbi'
+                input[2] = 'amrfinderplus'
+                input[3] = '--hamronized'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("argnorm - amrfinderplus_ncbi_hamronized - tsv - stub") {
+        options "-stub"
+
+        when {
+            process {
+                """                
+                input[0] = [
+                    [ id:'test.tsv', single_end:false ], // meta map                                                                                                                           
+                    file("https://raw.githubusercontent.com/BigDataBiology/argNorm/main/examples/hamronized/amrfinderplus.ncbi.orfs.tsv", checkIfExists: true)                              
+                ]
+                input[1] = 'ncbi'
+                input[2] = 'amrfinderplus'
+                input[3] = '--hamronized'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("argnorm - amrfinderplus_ncbi - tsv - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """                
+                input[0] = [
+                    [ id:'test.tsv', single_end:false ], // meta map                                                                                                                           
+                    file("https://raw.githubusercontent.com/BigDataBiology/argNorm/main/examples/raw/amrfinderplus.ncbi.orfs.tsv", checkIfExists: true)                              
+                ]
+                input[1] = 'ncbi'
+                input[2] = 'amrfinderplus'
+                input[3] = ''
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/argnorm/tests/main.nf.test.snap b/modules/nf-core/argnorm/tests/main.nf.test.snap
@@ -0,0 +1,142 @@
+{
+    "argnorm - amrfinderplus_ncbi_raw - tsv": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test.tsv",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,f870c239182592a065d9f80732b39bba"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,e200075d98a6f59137f105efceea0426"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test.tsv",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,f870c239182592a065d9f80732b39bba"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e200075d98a6f59137f105efceea0426"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-02T14:56:50.742114812"
+    },
+    "argnorm - amrfinderplus_ncbi_hamronized - tsv": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test.tsv",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,1f9a3820f09fd6a818af372dfe5cf322"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,e200075d98a6f59137f105efceea0426"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test.tsv",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,1f9a3820f09fd6a818af372dfe5cf322"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e200075d98a6f59137f105efceea0426"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-02T14:57:19.694510786"
+    },
+    "argnorm - amrfinderplus_ncbi_hamronized - tsv - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test.tsv",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,1f9a3820f09fd6a818af372dfe5cf322"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,e200075d98a6f59137f105efceea0426"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test.tsv",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,1f9a3820f09fd6a818af372dfe5cf322"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e200075d98a6f59137f105efceea0426"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-02T14:57:47.422476341"
+    },
+    "argnorm - amrfinderplus_ncbi - tsv - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test.tsv",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,e41b52c1213d8833c37472e3efb24db4"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,e200075d98a6f59137f105efceea0426"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test.tsv",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,e41b52c1213d8833c37472e3efb24db4"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e200075d98a6f59137f105efceea0426"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-02T14:58:14.950164297"
+    }
+}
diff --git a/modules/nf-core/argnorm/tests/tags.yml b/modules/nf-core/argnorm/tests/tags.yml
@@ -0,0 +1,2 @@
+argnorm:
+  - "modules/nf-core/argnorm/**"