Add module for Circlator (all)

modules/nf-core/any2fasta/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::any2fasta=0.8.1"

modules/nf-core/any2fasta/main.nf

@@ -0,0 +1,36 @@
+process ANY2FASTA {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/any2fasta:0.8.1--hdfd78af_0' :
+        'biocontainers/any2fasta:0.8.1--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(sequence)
+
+    output:
+    tuple val(meta), path("*.fasta"), emit: fasta
+    tuple val("${task.process}"), val('any2fasta'), eval("any2fasta -v 2>&1 | head -1 | sed 's/any2fasta //'"), topic: versions, emit: versions_any2fasta
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    any2fasta \\
+        $args \\
+        ${sequence} \\
+        > ${prefix}.fasta
+    """
+
+    stub:
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.fasta
+    """
+}

modules/nf-core/any2fasta/meta.yml

@@ -0,0 +1,70 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "any2fasta"
+description: Convert various sequence formats (GenBank, GFF, FASTQ, FASTA, CLUSTAL, Stockholm, GFA) to FASTA format. Input files may be gzip, bzip2, zip, or zstd compressed.
+keywords:
+  - fasta
+  - conversion
+  - sequences
+  - format
+  - genomics
+tools:
+  - "any2fasta":
+      description: "Convert various sequence formats to FASTA"
+      homepage: "https://github.com/tseemann/any2fasta"
+      documentation: "https://github.com/tseemann/any2fasta"
+      tool_dev_url: "https://github.com/tseemann/any2fasta"
+      licence:
+        - "GPL-3.0"
+      identifier: biotools:any2fasta
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - sequence:
+        type: file
+        description: |
+          Input sequence file in any supported format (GenBank, GFF, FASTQ, FASTA,
+          CLUSTAL, Stockholm, GFA). May be gzip, bzip2, zip, or zstd compressed.
+        pattern: "*.{gb,gbk,fa,fasta,fna,fq,fastq,gff,gfa,clw,sth,gb.gz,gbk.gz,fa.gz,fasta.gz,fq.gz,fastq.gz}"
+
+output:
+  fasta:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.fasta":
+          type: file
+          description: Output sequences in FASTA format
+          pattern: "*.fasta"
+  versions_any2fasta:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - any2fasta:
+          type: string
+          description: The name of the tool
+      - "any2fasta -v 2>&1 | head -1 | sed 's/any2fasta //'":
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - any2fasta:
+          type: string
+          description: The name of the tool
+      - "any2fasta -v 2>&1 | head -1 | sed 's/any2fasta //'":
+          type: eval
+          description: The expression to obtain the version of the tool
+
+authors:
+  - "@cwoodside1278"
+maintainers:
+  - "@cwoodside1278"

modules/nf-core/any2fasta/tests/main.nf.test

@@ -0,0 +1,85 @@
+nextflow_process {
+
+    name "Test Process ANY2FASTA"
+    script "../main.nf"
+    process "ANY2FASTA"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "any2fasta"
+
+    test("sarscov2 - fastq.gz") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - fasta") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - fastq.gz - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out
+                ).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/any2fasta/tests/main.nf.test.snap

@@ -0,0 +1,131 @@
+{
+    "sarscov2 - fastq.gz": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fasta:md5,f0c5c9110ce19e9ebbc9a6b6baf9e105"
+                    ]
+                ],
+                "1": [
+                    [
+                        "ANY2FASTA",
+                        "any2fasta",
+                        "0.8.1"
+                    ]
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fasta:md5,f0c5c9110ce19e9ebbc9a6b6baf9e105"
+                    ]
+                ],
+                "versions_any2fasta": [
+                    [
+                        "ANY2FASTA",
+                        "any2fasta",
+                        "0.8.1"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-03-20T22:41:21.33769732",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "sarscov2 - fastq.gz - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        "ANY2FASTA",
+                        "any2fasta",
+                        "0.8.1"
+                    ]
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_any2fasta": [
+                    [
+                        "ANY2FASTA",
+                        "any2fasta",
+                        "0.8.1"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-03-20T22:41:37.656452506",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "sarscov2 - fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fasta:md5,6e9fe4042a72f2345f644f239272b7e6"
+                    ]
+                ],
+                "1": [
+                    [
+                        "ANY2FASTA",
+                        "any2fasta",
+                        "0.8.1"
+                    ]
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fasta:md5,6e9fe4042a72f2345f644f239272b7e6"
+                    ]
+                ],
+                "versions_any2fasta": [
+                    [
+                        "ANY2FASTA",
+                        "any2fasta",
+                        "0.8.1"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-03-20T22:41:29.533525971",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    }
+}

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
+    """
+}