RiboCode - prepare_transcripts, metaplots, ribocode

modules/nf-core/ribocode/gtfupdate/environment.yml

@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::ribocode=1.2.15

modules/nf-core/ribocode/gtfupdate/main.nf

@@ -0,0 +1,38 @@
+process RIBOCODE_GTFUPDATE {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fe/fe815db0864b45b91afc7bc84c55cb60acb0035e7248dda7f480a55c4cb105d7/data':
+        'community.wave.seqera.io/library/ribocode:1.2.15--5530b252f5433a62' }"
+
+    input:
+    tuple val(meta), path(gtf)
+
+    output:
+    tuple val(meta), path("*.gtf")                                                  , emit: gtf
+    tuple val("${task.process}"), val('ribocode'), eval('RiboCode --version  2>&1') , emit: versions_ribocode, topic: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    GTFupdate \\
+        ${gtf} \\
+        $args \\
+        > ${prefix}_updated.gtf
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${prefix}_updated.gtf
+    """
+}

modules/nf-core/ribocode/gtfupdate/meta.yml

@@ -0,0 +1,66 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+name: "ribocode_gtfupdate"
+description: Update GTF annotation file for RiboCode compatibility
+keywords:
+  - ribo-seq
+  - ribosome profiling
+  - gtf
+  - annotation
+tools:
+  - "ribocode":
+      description: "A package for detecting the actively translated ORFs using ribosome-profiling
+        data"
+      homepage: "https://github.com/xryanglab/RiboCode"
+      documentation: "https://github.com/xryanglab/RiboCode"
+      tool_dev_url: "https://github.com/xryanglab/RiboCode"
+      doi: "10.1093/nar/gky179"
+      licence: ["MIT"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'test', single_end:false ]`
+    - gtf:
+        type: file
+        description: GTF annotation file to update (uncompressed)
+        pattern: "*.{gtf}"
+        ontologies: []
+output:
+  gtf:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*.gtf":
+          type: file
+          description: Updated GTF annotation file
+          pattern: "*_updated.gtf"
+  versions_ribocode:
+    - - ${task.process}:
+          type: string
+          description: Name of the process
+      - ribocode:
+          type: string
+          description: Name of the tool
+      - RiboCode --version  2>&1:
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: Name of the process
+      - ribocode:
+          type: string
+          description: Name of the tool
+      - RiboCode --version  2>&1:
+          type: eval
+          description: The expression to obtain the version of the tool
+
+authors:
+  - "@JackCurragh"

modules/nf-core/ribocode/gtfupdate/tests/main.nf.test

@@ -0,0 +1,56 @@
+nextflow_process {
+
+    name "Test Process RIBOCODE_GTFUPDATE"
+    script "../main.nf"
+    process "RIBOCODE_GTFUPDATE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "ribocode"
+    tag "ribocode/gtfupdate"
+
+    test("test_ribocode_gtfupdate") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/Homo_sapiens.GRCh38.111_chr20.gtf", checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match("process_outputs") },
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match("versions") }
+            )
+        }
+    }
+
+    test("test_ribocode_gtfupdate - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/Homo_sapiens.GRCh38.111_chr20.gtf", checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.gtf[0][1].toString().endsWith('.gtf') }
+            )
+        }
+    }
+}

modules/nf-core/ribocode/gtfupdate/tests/main.nf.test.snap

@@ -0,0 +1,61 @@
+{
+    "versions": {
+        "content": [
+            {
+                "versions_ribocode": [
+                    [
+                        "RIBOCODE_GTFUPDATE",
+                        "ribocode",
+                        "1.2.15"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2025-12-15T13:58:20.352527"
+    },
+    "process_outputs": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_updated.gtf:md5,4aee3722f1d061395e2fdce7277708b3"
+                    ]
+                ],
+                "1": [
+                    [
+                        "RIBOCODE_GTFUPDATE",
+                        "ribocode",
+                        "1.2.15"
+                    ]
+                ],
+                "gtf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_updated.gtf:md5,4aee3722f1d061395e2fdce7277708b3"
+                    ]
+                ],
+                "versions_ribocode": [
+                    [
+                        "RIBOCODE_GTFUPDATE",
+                        "ribocode",
+                        "1.2.15"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2025-12-15T13:58:20.062134"
+    }
+}

modules/nf-core/ribocode/metaplots/environment.yml

@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::ribocode=1.2.15

modules/nf-core/ribocode/metaplots/main.nf

@@ -0,0 +1,40 @@
+process RIBOCODE_METAPLOTS {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fe/fe815db0864b45b91afc7bc84c55cb60acb0035e7248dda7f480a55c4cb105d7/data':
+        'community.wave.seqera.io/library/ribocode:1.2.15--5530b252f5433a62' }"
+
+    input:
+    tuple val(meta), path(bam)
+    tuple val(meta2), path(annotation)
+
+    output:
+    tuple val(meta), path("*config.txt")                                            , emit: config
+    tuple val(meta), path("*.pdf")                                                  , emit: pdf
+    tuple val("${task.process}"), val('ribocode'), eval('RiboCode --version  2>&1') , emit: versions_ribocode, topic: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    metaplots \\
+        -a $annotation \\
+        -r $bam \\
+        -o ${prefix} \\
+        $args
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_config.txt
+    touch ${prefix}_report.pdf
+    """
+}

modules/nf-core/ribocode/metaplots/meta.yml

@@ -0,0 +1,87 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+name: "ribocode_metaplots"
+description: Set up RiboCode ORF calling with metaplots
+keywords:
+  - ribo-seq
+  - ribosome profiling
+  - orf calling
+tools:
+  - "ribocode":
+      description: "A package for detecting the actively translated ORFs using ribosome-profiling
+        data"
+      homepage: "https://github.com/xryanglab/RiboCode"
+      documentation: "https://github.com/xryanglab/RiboCode"
+      tool_dev_url: "https://github.com/xryanglab/RiboCode"
+      doi: "10.1093/nar/gky179"
+      licence: ["MIT"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'test', single_end:false ]`
+    - bam:
+        type: file
+        description: Sorted BAM/CRAM/SAM file
+        pattern: "*.{bam,cram,sam}"
+        ontologies: []
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing annotation information
+          e.g. `[ id:'genome' ]`
+    - annotation:
+        type: directory
+        description: Directory containing annotation files from ribocode/prepare
+        pattern: "annotation"
+
+output:
+  config:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*config.txt":
+          type: file
+          description: RiboCode configuration file containing P-site offsets
+          pattern: "*_config.txt"
+          ontologies: []
+  pdf:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*.pdf":
+          type: file
+          description: PDF file containing P-site metaplots for quality control
+          pattern: "*_report.pdf"
+          ontologies: []
+  versions_ribocode:
+    - - ${task.process}:
+          type: string
+          description: Name of the process
+      - ribocode:
+          type: string
+          description: Name of the tool
+      - RiboCode --version  2>&1:
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: Name of the process
+      - ribocode:
+          type: string
+          description: Name of the tool
+      - RiboCode --version  2>&1:
+          type: eval
+          description: The expression to obtain the version of the tool
+
+authors:
+  - "@JackCurragh"