New module: Ribodetector

modules/nf-core/ribodetector/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::ribodetector=0.3.1"

modules/nf-core/ribodetector/main.nf

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+process RIBODETECTOR {
+	tag "$meta.id"
+	label 'process_medium'
+
+	conda "${moduleDir}/environment.yml"
+	container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+		'https://depot.galaxyproject.org/singularity/ribodetector:0.3.1--pyhdfd78af_0':
+		'biocontainers/ribodetector:0.3.1--pyhdfd78af_0' }"
+
+	input:
+	tuple val(meta), path(fastq)
+	val length
+
+	output:
+	tuple val(meta), path("*.nonrna*.fastq.gz"), emit: fastq
+	tuple val(meta), path("*.log")             , emit: log
+	path "versions.yml"                        , emit: versions
+
+	when:
+	task.ext.when == null || task.ext.when
+
+	script:
+	def args = task.ext.args ?: ''
+	def prefix = task.ext.prefix ?: "${meta.id}"
+	ribodetector_bin = task.accelerator ? "ribodetector" : "ribodetector_cpu"
+	ribodetector_mem = task.accelerator ? "-m $task.memory.toGiga()" : ""
+	output = meta.single_end ? "${prefix}.nonrna.fastq.gz" : "${prefix}.nonrna.1.fastq.gz ${prefix}.nonrna.2.fastq.gz"
+
+	"""
+	${ribodetector_bin} \\
+		-i ${fastq} \\
+		-o ${output} \\
+		-l ${length} \\
+		-t ${task.cpus} \\
+		--log ${prefix}.log \\
+		${ribodetector_mem} \\
+		${args}
+
+	cat <<-END_VERSIONS > versions.yml
+	"${task.process}":
+		ribodetector: \$(ribodetector --version | sed 's/ribodetector //g')
+	END_VERSIONS
+	"""
+
+	stub:
+	def args = task.ext.args ?: ''
+	def prefix = task.ext.prefix ?: "${meta.id}"
+
+	"""
+	echo $args
+
+	echo | gzip > ${prefix}.nonrna.1.fastq.gz  
+    echo | gzip > ${prefix}.nonrna.2.fastq.gz  
+	touch ${prefix}.log
+
+	cat <<-END_VERSIONS > versions.yml
+	"${task.process}":
+		ribodetector: \$(ribodetector --version | sed 's/ribodetector //g')
+	END_VERSIONS
+	"""
+}

modules/nf-core/ribodetector/meta.yml

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+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "ribodetector"
+description: Accurate and rapid RiboRNA sequences Detector based on deep 
+  learning
+keywords:
+- RNA
+- RNAseq
+- rRNA
+- ribosomal RNA
+- rRNA depletion
+- rRNA removal
+- rRNA filtering
+- deep learning
+- Riboseq
+- genomics
+tools:
+- "ribodetector":
+    description: "Accurate and rapid RiboRNA sequences detector based on deep learning"
+    homepage: "https://github.com/hzi-bifo/RiboDetector"
+    documentation: "https://github.com/hzi-bifo/RiboDetector"
+    tool_dev_url: "https://github.com/hzi-bifo/RiboDetector"
+    doi: "10.1093/nar/gkac112"
+    licence: ['GPL v3-or-later']
+    identifier: biotools:ribodetector
+
+input:
+- - meta:
+      type: map
+      description: |
+        Groovy Map containing riboseq sample information
+        e.g. `[ id:'sample1', single_end:false ]
+  - fastq:
+      type: file
+      description: |
+        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+        respectively.
+      ontologies:
+      - edam: http://edamontology.org/format_1930     # fastq format
+- length: 
+    type: integer
+    description: |
+      Sequencing read length (mean length). Note: the accuracy reduces for reads shorter than 40
+    pattern: "integer >= 1"
+output:
+  fastq:
+  - - meta:
+        type: map
+        description: Groovy Map containing sample information
+    - "*.nonrna*.fastq.gz":
+        type: file
+        description: rRNA depleted FastQ files
+        pattern: "*.nonrna*.fastq.gz"
+        ontologies:
+        - edam: http://edamontology.org/format_1930     # fastq format
+        - edam: http://edamontology.org/format_3989  # GZIP format
+  log:
+  - - meta:
+        type: map
+        description: Groovy Map containing sample information
+    - "*.log":
+        type: file
+        description: Log file from RiboDetector
+        pattern: "*.log"
+        ontologies: []
+  versions:
+  - versions.yml:
+      type: file
+      description: File containing software versions
+      pattern: versions.yml
+      ontologies:
+      - edam: http://edamontology.org/format_3750      # YAML
+authors:
+- "@maxibor"
+maintainers:
+- "@maxibor"

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

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+nextflow_process {
+
+    name "Test Process RIBODETECTOR"
+    script "../main.nf"
+    process "RIBODETECTOR"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "ribodetector"
+
+    test("ribodetector - rnaseq PE input") {
+        when {
+            process {
+                """
+               input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ]
+                input[1] = 150
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.fastq },
+                { assert process.out.log },
+                { assert path(process.out.log[0][1]).getText().contains("Writing output non-rRNA sequences") },
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+
+    }
+
+    test("ribodetector - stub rnaseq PE input") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
+                    ]
+                ]
+                input[1] = 150
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

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

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+{
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,f98df8f0eaa704e4db74785adc9cc791"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-10-27T10:12:20.183608"
+    },
+    "ribodetector - stub rnaseq PE input": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.nonrna.1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test.nonrna.2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,f98df8f0eaa704e4db74785adc9cc791"
+                ],
+                "fastq": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.nonrna.1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test.nonrna.2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f98df8f0eaa704e4db74785adc9cc791"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-10-27T10:12:59.627863"
+    }
+}