RiboCode - prepare_transcripts, metaplots, ribocode

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

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::ribocode=1.2.15

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

@@ -0,0 +1,50 @@
+process RIBOCODE_METAPLOTS {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ribocode:1.2.15--pyhfa5458b_0':
+        'biocontainers/ribocode:1.2.15--pyhfa5458b_0' }"
+
+    input:
+    tuple val(meta), path(bam)
+    path annotation
+
+    output:
+    tuple val(meta), path("*config.txt")             , emit: config
+    tuple val(meta), path("*.pdf")                  , emit: pdf
+    path "versions.yml"                             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    metaplots \\
+        -a $annotation \\
+        -r $bam \\
+        -o ${prefix} \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        RiboCode: \$(RiboCode --version 2>&1)
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_config.txt
+    touch ${prefix}_report.pdf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        RiboCode: \$(echo "1.2.15")
+    END_VERSIONS
+    """
+}

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

@@ -0,0 +1,64 @@
+# 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: []
+  - annotation:
+      type: directory
+      description: Directory containing annotation files
+      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:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+authors:
+  - "@JackCurragh"

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

@@ -0,0 +1,51 @@
+nextflow_process {
+
+    name "Test Process RIBOCODE_METAPLOTS"
+    script "../main.nf"
+    process "RIBOCODE_METAPLOTS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "ribocode"
+    tag "ribocode/metaplots"
+    tag "ribocode/prepare"
+
+    setup {
+        run("RIBOCODE_PREPARE") {
+            script "../../prepare/main.nf"
+            process {
+
+                """
+                input[0] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/Homo_sapiens.GRCh38.dna.chromosome.20.fa.gz", checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/Homo_sapiens.GRCh38.111_chr20.gtf", checkIfExists: true)
+                """
+            }
+        }
+    }
+
+    test("test_ribocode_metaplots") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ],
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/aligned_reads/SRX11780887.Aligned.toTranscriptome.out.bam", checkIfExists: true)
+                ]
+                input[1] = RIBOCODE_PREPARE.out.annotation
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

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

@@ -0,0 +1,55 @@
+{
+    "test_ribocode_metaplots": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_pre_config.txt:md5,6da5a4583c1f94ec908c9556bf7064be"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "testSRX11780887.Aligned.toTranscriptome.out.pdf:md5,464c91bb5532a571ed2c9c6ae6403a86"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,7e9b4c67f04dd073e78f174e1e41720c"
+                ],
+                "config": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_pre_config.txt:md5,6da5a4583c1f94ec908c9556bf7064be"
+                    ]
+                ],
+                "pdf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "testSRX11780887.Aligned.toTranscriptome.out.pdf:md5,464c91bb5532a571ed2c9c6ae6403a86"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7e9b4c67f04dd073e78f174e1e41720c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-12-01T15:29:32.897378"
+    }
+}

modules/nf-core/ribocode/metaplots/tests/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    withName: RIBOCODE_METAPLOTS {
+        ext.args = '-f0_percent 0.1 -pv1 1 -pv2 1'
+    }
+}

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

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::ribocode=1.2.15

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

@@ -0,0 +1,64 @@
+process RIBOCODE_PREPARE {
+    tag "$fasta"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ribocode:1.2.15--pyhfa5458b_0':
+        'biocontainers/ribocode:1.2.15--pyhfa5458b_0' }"
+
+    input:
+    path fasta
+    path gtf
+
+    output:
+    path "annotation"             , emit: annotation
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+
+    """
+    # nf-core: ensure FASTA is uncompressed
+    GENOME="$fasta"
+    if [[ "\$GENOME" == *.gz ]]; then
+        gunzip -c "\$GENOME" > genome.fa
+        GENOME="genome.fa"
+    fi
+
+    # Update the GTF
+    GTFupdate \\
+        $gtf  \\
+        > updated.gtf
+
+    # Run prepare_transcripts with uncompressed FASTA
+    prepare_transcripts \\
+        -g updated.gtf \\
+        -f "\$GENOME" \\
+        -o annotation
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        RiboCode: \$(RiboCode --version)
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+
+    """
+    mkdir annotation
+
+    touch annotation/transcripts_cds.txt
+    touch annotation/transcripts_sequence.fa
+    touch annotation/transcripts.pickle
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        RiboCode: \$(echo "1.2.15")
+    END_VERSIONS
+    """
+}

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

@@ -0,0 +1,45 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+name: "ribocode_prepare"
+description: Prepare the annotation files for RiboCode ORF calling
+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:
+  - fasta:
+      type: file
+      description: Reference genome FASTA file
+      pattern: "*.{fasta,fa,fna}"
+      ontologies: []
+  - gtf:
+      type: file
+      description: Reference genome GTF annotation file
+      pattern: "*.{gtf}"
+
+      ontologies: []
+output:
+  annotation:
+    - annotation:
+        type: directory
+        description: Directory containing RiboCode annotation files
+          (transcripts_cds.txt, transcripts_sequence.fa, transcripts.pickle)
+        pattern: "annotation/"
+
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+authors:
+  - "@JackCurragh"

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

@@ -0,0 +1,32 @@
+nextflow_process {
+
+    name "Test Process RIBOCODE_PREPARE"
+    script "../main.nf"
+    process "RIBOCODE_PREPARE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "ribocode"
+    tag "ribocode/prepare"
+
+    test("test_ribocode_prepare") {
+
+        when {
+            process {
+                """
+                input[0] = file(params.modules_testdata_base_path + "genomics/homo_sapiens/riboseq_expression/Homo_sapiens.GRCh38.dna.chromosome.20.fa.gz", checkIfExists: true)
+                input[1] = 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() }
+            )
+        }
+
+    }
+
+}