Rattle cluster

modules/nf-core/rattle/cluster/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::false_flag

modules/nf-core/rattle/cluster/main.nf

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+process RATTLE_CLUSTER {
+    tag "$meta.id"
+    label 'process_low'
+
+    if (params.enable_conda) {
+        error "Conda environments are not set up for rattle (when this module was built). Please use docker or singularity containers."
+    }
+    container 'ecoflowucl/rattle:v1.0'
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path("clusters.out"), emit: clusters
+    path "versions.yml"                  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def RATTLE_VERSION = "v1.0" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    rattle \\
+        cluster $args \\
+        -t $task.cpus \\
+        -i $reads
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        rattle: $RATTLE_VERSION
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch clusters.out
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        rattle: $RATTLE_VERSION
+    END_VERSIONS
+    """
+}

modules/nf-core/rattle/cluster/meta.yml

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+name: "rattle_cluster"
+description: Reference-free reconstruction and quantification of transcriptomes from
+  long-read sequencing
+keywords:
+  - transcriptomes
+  - cluster
+  - nanopore
+tools:
+  - "rattle":
+      description: "Reference-free reconstruction and quantification of transcriptomes
+        from long-read sequencing"
+      homepage: "https://github.com/comprna/RATTLE"
+      documentation: "https://github.com/comprna/RATTLE"
+      tool_dev_url: "https://github.com/comprna/RATTLE"
+      doi: "10.1186/s13059-022-02715-w"
+      licence: ["GPL-3.0"]
+      identifier: biotools:rattle
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', suffix:'bacteria' ]`
+    - reads:
+        type: file
+        description: Input file in FASTA/FASTQ format.
+        pattern: "*.{fasta,fastq,fasta.gz,fastq.gz,fa,fq,fa.gz,fq.gz}"
+output:
+  - clusters:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', suffix:'bacteria' ]
+    - "clusters.out":
+          type: file
+          description: Output clusters in binary format.
+          pattern: "cluster.out"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@chriswyatt1"
+maintainers:
+  - "@chriswyatt1"

modules/nf-core/rattle/cluster/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process RATTLE_CLUSTER"
+    script "../main.nf"
+    process "RATTLE_CLUSTER"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "rattle"
+    tag "rattle/cluster"
+
+    test("test-rattle") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    [ file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/nanopore/fastq/test.fastq.gz', checkIfExists: true) ]
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

modules/nf-core/rattle/cluster/tests/main.nf.test.snap

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+{
+    "test-rattle": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "clusters.out:md5,809306985afaace6a2a107d33d4784c7"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d8ac60817803edd53da602b602061e4d"
+                ],
+                "clusters": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "clusters.out:md5,809306985afaace6a2a107d33d4784c7"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d8ac60817803edd53da602b602061e4d"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-06T14:00:48.224614821"
+    }
+}