add crabs/downloadtaxonomy as module

modules/nf-core/crabs/downloadtaxonomy/environment.yml

@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::crabs=1.0.7"

modules/nf-core/crabs/downloadtaxonomy/main.nf

@@ -0,0 +1,53 @@
+process CRABS_DOWNLOADTAXONOMY {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/crabs:1.0.7--pyhdfd78af_0':
+        'biocontainers/crabs:1.0.7--pyhdfd78af_0' }"
+
+    input:
+    val(meta)
+
+    output:
+    tuple val(meta), path("*/nucl_gb.accession2taxid"), emit: accession2taxid
+    tuple val(meta), path("*/names.dmp")              , emit: names
+    tuple val(meta), path("*/nodes.dmp")              , emit: nodes
+    tuple val(meta), path("*")                        , emit: downloadtaxonomy_dir
+    path "versions.yml"                               , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir ${prefix}
+
+    crabs --download-taxonomy \\
+        --output ${prefix} \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        crabs: \$(crabs --help | grep 'CRABS |' | sed 's/.*CRABS | \\(v[0-9.]*\\).*/\\1/')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir ${prefix}
+    touch ${prefix}/nucl_gb.accession2taxid
+    touch ${prefix}/names.dmp
+    touch ${prefix}/nodes.dmp
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        crabs: \$(crabs --help | grep 'CRABS |' | sed 's/.*CRABS | \\(v[0-9.]*\\).*/\\1/')
+    END_VERSIONS
+    """
+}

modules/nf-core/crabs/downloadtaxonomy/meta.yml

@@ -0,0 +1,69 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "crabs_downloadtaxonomy"
+## TODO nf-core: Add a description of the module and list keywords
+description: write your description here
+keywords:
+  - sort
+  - example
+  - genomics
+tools:
+  - "crabs":
+      ## TODO nf-core: Add a description and other details for the software below
+      description: "Crabs (Creating Reference databases for Amplicon-Based Sequencing) is a program to download and curate reference databases for eDNA metabarcoding analyses."
+      homepage: "None"
+      documentation: "None"
+      tool_dev_url: "https://github.com/gjeunen/reference_database_creator"
+      doi: ""
+      licence: ['MIT']
+      identifier: 
+
+## TODO nf-core: Add a description of all of the variables used as input
+input:
+  # Only when we have meta
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+
+  ## TODO nf-core: Delete / customise this example input
+    - bam:
+        type: file
+        description: Sorted BAM/CRAM/SAM file
+        pattern: "*.{bam,cram,sam}"
+        ontologies:
+          - edam: "http://edamontology.org/format_25722"
+          - edam: "http://edamontology.org/format_2573"
+          - edam: "http://edamontology.org/format_3462"
+
+
+## TODO nf-core: Add a description of all of the variables used as output
+output:
+  - bam:
+  #Only when we have meta
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+  ## TODO nf-core: Delete / customise this example output
+    - "*.bam":
+        type: file
+        description: Sorted BAM/CRAM/SAM file
+        pattern: "*.{bam,cram,sam}"
+        ontologies:
+          - edam: "http://edamontology.org/format_25722"
+          - edam: "http://edamontology.org/format_2573"
+          - edam: "http://edamontology.org/format_3462"
+
+  - versions:
+    - "versions.yml":
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+
+authors:
+  - "@famosab"
+maintainers:
+  - "@famosab"

modules/nf-core/crabs/downloadtaxonomy/tests/main.nf.test

@@ -0,0 +1,58 @@
+nextflow_process {
+
+    name "Test Process CRABS_DOWNLOADTAXONOMY"
+    script "../main.nf"
+    process "CRABS_DOWNLOADTAXONOMY"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "crabs"
+    tag "crabs/downloadtaxonomy"
+
+    test("download") {
+
+        when {
+            params {
+                module_args = "--exclude 'acc2taxid,taxdump'"
+            }
+            process {
+                """
+                input[0] = [ id:'test' ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("download - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ id:'test' ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                    ).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/crabs/downloadtaxonomy/tests/main.nf.test.snap

@@ -0,0 +1,137 @@
+{
+    "download": {
+        "content": [
+            {
+                "0": [
+
+                ],
+                "1": [
+
+                ],
+                "2": [
+
+                ],
+                "3": [
+
+                ],
+                "accession2taxid": [
+
+                ],
+                "names": [
+
+                ],
+                "nodes": [
+
+                ],
+                "versions": [
+
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-03T13:56:49.20584"
+    },
+    "download - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "nucl_gb.accession2taxid:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "names.dmp:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "nodes.dmp:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            [
+                                "names.dmp:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "nodes.dmp:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "nucl_gb.accession2taxid:md5,d41d8cd98f00b204e9800998ecf8427e"
+                            ],
+                            "versions.yml:md5,b98b46449a638f8825d42a6abe7a742e"
+                        ]
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,b98b46449a638f8825d42a6abe7a742e"
+                ],
+                "accession2taxid": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "nucl_gb.accession2taxid:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "downloadtaxonomy_dir": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            [
+                                "names.dmp:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "nodes.dmp:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                "nucl_gb.accession2taxid:md5,d41d8cd98f00b204e9800998ecf8427e"
+                            ],
+                            "versions.yml:md5,b98b46449a638f8825d42a6abe7a742e"
+                        ]
+                    ]
+                ],
+                "names": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "names.dmp:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "nodes": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "nodes.dmp:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b98b46449a638f8825d42a6abe7a742e"
+                ]
+            },
+            {
+                "CRABS_DOWNLOADTAXONOMY": {
+                    "crabs": "v1.0.7"
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-03T14:07:27.923472"
+    }
+}

modules/nf-core/crabs/downloadtaxonomy/tests/nextflow.config

@@ -0,0 +1,7 @@
+process {
+
+    withName: 'CRABS_DOWNLOADTAXONOMY' {
+        ext.args = params.module_args
+    }
+
+}