Anarcii

modules/nf-core/anarcii/environment.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "conda-forge::pip=26.0.1"
+  - pip:
+      - anarcii==2.0.5

modules/nf-core/anarcii/main.nf

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+process ANARCII {
+    tag "${meta.id}"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine == 'singularity'
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c5/c56cb3320588978063f0893876f4f2b6f088dadc75628f60a746ee54e72350a6/data'
+        : 'community.wave.seqera.io/library/python_pip_anarcii:4e5c3ffabd22d3fc'}"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*.csv"), emit: anarcii
+    tuple val("${task.process}"), val('anarcii'), eval('anarcii --version | sed "s/^anarcii //"'), topic: versions, emit: versions_anarcii
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    anarcii \\
+        ${args}\\
+        -o ${prefix}.csv \\
+        ${fasta}
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo ${args}
+
+    touch ${prefix}.csv
+    """
+}

modules/nf-core/anarcii/meta.yml

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+name: "anarcii"
+description: A language model for antigen receptor numbering
+keywords:
+  - annotate
+  - antibody
+  - TCR
+  - immunology
+tools:
+  - "anarcii":
+      description: "A language model for antigen receptor numbering"
+      homepage: "https://github.com/oxpig/ANARCII"
+      documentation: "https://github.com/oxpig/ANARCII/wiki"
+      tool_dev_url: "https://github.com/oxpig/ANARCII"
+      doi: "10.5281/zenodo.15274840"
+      licence:
+        - "BSD 3-Clause License"
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - fasta:
+        type: file
+        description: Fasta file with full receptor sequences
+        pattern: "*.fasta"
+        ontologies:
+          - edam: http://edamontology.org/format_1929
+output:
+  anarcii:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.csv":
+          type: file
+          description: File containing per-base numbering
+          pattern: "*.csv"
+          ontologies:
+            - edam: http://edamontology.org/format_3752
+  versions_anarcii:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - anarcii:
+          type: string
+          description: The name of the tool
+      - anarcii --version | sed "s/^anarcii //":
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - anarcii:
+          type: string
+          description: The name of the tool
+      - anarcii --version | sed "s/^anarcii //":
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@Clara0611"
+maintainers:
+  - "@Clara0611"

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

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+// nf-core modules test anarcii
+nextflow_process {
+
+    name "Test Process ANARCII"
+    script "../main.nf"
+    process "ANARCII"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "anarcii"
+
+    test("human - fasta") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/anarcii/anarcii_vdjdb.fasta', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            def anarciiResults = path(process.out.anarcii.get(0).get(1)).csv
+            assert "Name" in anarciiResults.columnNames
+            assert "Chain" in anarciiResults.columnNames
+            assert "Score" in anarciiResults.columnNames
+            assert "Query start" in anarciiResults.columnNames
+            assert "Query end" in anarciiResults.columnNames
+        }
+    }
+
+    test("human - fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/anarcii/anarcii_vdjdb.fasta', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+
+    }
+
+}

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

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+{
+    "human - fasta - stub": {
+        "content": [
+            {
+                "anarcii": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_anarcii": [
+                    [
+                        "ANARCII",
+                        "anarcii",
+                        "2.0.5"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-04-01T14:42:12.168257534",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    }
+}