Add circlator/all module

modules/nf-core/circlator/all/environment.yml

@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::circlator=1.5.5"

modules/nf-core/circlator/all/main.nf

@@ -0,0 +1,40 @@
+process CIRCLATOR_ALL {
+    tag "$meta.id"
+    label 'process_high'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+       'https://depot.galaxyproject.org/singularity/circlator:1.5.5--py35_0':
+       'biocontainers/circlator:1.5.5--py35_0' }"
+
+    input:
+    tuple val(meta), path(assembly)
+    tuple val(meta2), path(reads)
+
+    output:
+    tuple val(meta), path("${prefix}"),        emit: results
+    tuple val(meta), path("${prefix}/*.fasta"), emit: fasta
+    tuple val("${task.process}"), val('circlator'), eval("circlator version"), topic: versions, emit: versions_circlator
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    circlator all \\
+        $args \\
+        --threads $task.cpus \\
+        ${assembly} \\
+        ${reads} \\
+        ${prefix}
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir -p ${prefix}
+    touch ${prefix}/06.fixstart.fasta
+    """
+}

modules/nf-core/circlator/all/meta.yml

@@ -0,0 +1,94 @@
+name: "circlator_all"
+description: >
+  Runs the full Circlator pipeline to circularise genome assemblies from long reads.
+  Sequentially runs: mapreads, bam2reads, assemble, merge, clean, and fixstart.
+keywords:
+  - circlator
+  - genome assembly
+  - circularisation
+  - long reads
+  - genomics
+tools:
+  - "circlator":
+      description: "A tool to circularise genome assemblies using long sequencing reads."
+      homepage: "https://github.com/sanger-pathogens/circlator"
+      documentation: "https://github.com/sanger-pathogens/circlator/wiki"
+      tool_dev_url: "https://github.com/sanger-pathogens/circlator"
+      doi: "10.1186/s13059-015-0849-0"
+      licence:
+        - "GPL v3"
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - assembly:
+        type: file
+        description: Input genome assembly in FASTA format
+        pattern: "*.{fasta,fa,fna}"
+        ontologies:
+          - edam: "http://edamontology.org/format_1929"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information for reads
+          e.g. `[ id:'sample1' ]`
+    - reads:
+        type: file
+        description: Long reads in FASTA or FASTQ format (PacBio or Oxford
+          Nanopore)
+        pattern: "*.{fasta,fa,fastq,fq}"
+        ontologies:
+          - edam: "http://edamontology.org/format_1929"
+          - edam: "http://edamontology.org/format_1930"
+output:
+  results:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - ${prefix}:
+          type: directory
+          description: Directory containing all intermediate and final output
+            files from Circlator
+          pattern: "*"
+  fasta:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - ${prefix}/*.fasta:
+          type: file
+          description: Final circularised genome assembly in FASTA format
+          pattern: "*.fasta"
+          ontologies:
+            - edam: "http://edamontology.org/format_1929"
+  versions_circlator:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - circlator:
+          type: string
+          description: The name of the tool
+      - circlator version:
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - circlator:
+          type: string
+          description: The name of the tool
+      - circlator version:
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@cwoodside1278"
+maintainers:
+  - "@cwoodside1278"

modules/nf-core/circlator/all/tests/main.nf.test

@@ -0,0 +1,33 @@
+nextflow_process {
+    name "Test Process CIRCLATOR_ALL"
+    script "../main.nf"
+    process "CIRCLATOR_ALL"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "circlator"
+    tag "circlator/all"
+
+    test("sarscov2 - fasta reads - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

modules/nf-core/circlator/all/tests/main.nf.test.snap

@@ -0,0 +1,63 @@
+{
+    "sarscov2 - fasta reads - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "06.fixstart.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "06.fixstart.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        "CIRCLATOR_ALL",
+                        "circlator",
+                        "1.5.5"
+                    ]
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "06.fixstart.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "results": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "06.fixstart.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions_circlator": [
+                    [
+                        "CIRCLATOR_ALL",
+                        "circlator",
+                        "1.5.5"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-03-22T18:50:56.053731566",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    }
+}