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JackCurraghpinin4fjordsclaude
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RiboCode - prepare_transcripts, metaplots, ribocode (#9485)
* add 3 required ribocode modules * GTFUpdate; meta in inputs; No Gzip; * return snaps * nf-test passing * Update RiboCode versions to use topics * Update RiboCode versions to use topics -New lines at EOF * Update RiboCode versions to use topics - Prettier * RiboCode update snapshots * Update RiboCode snapshots to container versions * Bump to latest ribocode build with pyfasta and ribocode fixes * Improve RiboCode module tests and fix review issues - Remove defaults channel from environment.yml files - Fix keywords to lowercase in meta.yml files - Add stub tests to all modules - Update version snapshots from 1.2.14 to 1.2.15 - Remove duplicate snapshot entries - Optimize test setup using pre-made test data: - metaplots/ribocode: use UNTAR for annotation instead of full setup chain - prepare: use pre-made updated GTF instead of running gtfupdate Temporarily points to test-datasets branch pending merge of: nf-core/test-datasets#1820 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * Update RiboCode snapshot to GHA runner architecture Update md5 hashes to match linux/amd64 output from CI runners. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * Add schema reference to ribocode/ribocode meta.yml 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * Revert nf-test.config to standard test-datasets paths test-datasets PR #1820 has been merged, reverting to nf-core/test-datasets. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> --------- Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
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‎modules/nf-core/ribocode/gtfupdate/environment.yml‎

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channels:
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- conda-forge
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- bioconda
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dependencies:
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- bioconda::ribocode=1.2.15

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

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

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

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

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

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

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

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

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

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channels:
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- conda-forge
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- bioconda
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dependencies:
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- bioconda::ribocode=1.2.15

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

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

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

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

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