nf-core · JackCurragh · Dec 16, 2025 · Dec 16, 2025 · Dec 16, 2025 · Dec 16, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,16 +9,22 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#125](https://github.com/nf-core/riboseq/pull/125) - Add rRNA removal tool selection with support for SortMeRNA (default), Bowtie2, and RiboDetector ([@pinin4fjords](https://github.com/pinin4fjords))
 - [#131](https://github.com/nf-core/riboseq/pull/131) - Add ribotish quality output routing to MultiQC ([@pinin4fjords](https://github.com/pinin4fjords))
+- Add RiboCode ORF detection with P-site analysis and metaplots ([@JackCurragh](https://github.com/JackCurragh))
 
 ### `Changed`
 
 - [#129](https://github.com/nf-core/riboseq/pull/129) - Bump pipeline version to 1.3.0dev ([@iraiosub](https://github.com/iraiosub))
 
 ### `Parameters`
 
-| Old parameter | New parameter         |
-| ------------- | --------------------- |
-|               | `--ribo_removal_tool` |
+| Old parameter | New parameter                      |
+| ------------- | ---------------------------------- |
+|               | `--ribo_removal_tool`              |
+|               | `--skip_ribocode`                  |
+|               | `--extra_ribocode_gtfupdate_args`  |
+|               | `--extra_ribocode_prepare_args`    |
+|               | `--extra_ribocode_metaplots_args`  |
+|               | `--extra_ribocode_ribocode_args`   |
 
 ### `Dependencies`
 

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -40,6 +40,10 @@
 
   > Choudhary S, Li W, D Smith A. Accurate detection of short and long active ORFs using Ribo-seq data. Bioinformatics. 2020 Apr 1;36(7):2053-2059. doi: 10.1093/bioinformatics/btz878. PMID: 31750902; PMCID: PMC7141849.
 
+- [RiboCode](https://pubmed.ncbi.nlm.nih.gov/29538776/)
+
+  > Zhengtao Xiao, Rongyao Huang, Xudong Xing, Yuling Chen, Haiteng Deng, Xuerui Yang. De novo annotation and characterization of the translatome with ribosome profiling data Nucleic Acids Res. 2018 Jun 1;46(10):e61. doi: 10.1093/nar/gky179. PMID: 29538776 PMCID: PMC6007384 
+
 - [riboWaltz](https://pubmed.ncbi.nlm.nih.gov/30102689/)
 
   > Lauria F, Tebaldi T, Bernabò P, Groen EJN, Gillingwater TH, Viero G. riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data. PLoS Comput Biol. 2018 Aug 13;14(8):e1006169. doi: 10.1371/journal.pcbi.1006169. PMID: 30102689; PMCID: PMC6112680.

diff --git a/README.md b/README.md
@@ -41,8 +41,9 @@ Differences occur in the downstream analysis steps. Currently these specialist s
 1. Check reads distribution around annotated protein coding regions on user provided transcripts, show frame bias and estimate P-site offset for different group of reads ([`Ribo-TISH`](https://github.com/zhpn1024/ribotish))
 2. (default, optional) Predict translated open reading frames and/ or translation initiation sites _de novo_ from alignment data ([`Ribo-TISH`](https://github.com/zhpn1024/ribotish))
 3. (default, optional) Derive candidate ORFs from reference data and detect translated ORFs from that list ([`Ribotricer`](https://github.com/smithlabcode/ribotricer))
-4. (default, optional) Derive P-sites and QC from transcriptome alignments ([`riboWaltz`](https://github.com/LabTranslationalArchitectomics/riboWaltz))
-5. (optional) Use a translational efficiency approach to study the dynamics of transcription and translation, with [anota2seq](https://bioconductor.org/packages/release/bioc/html/anota2seq.html). **requires matched RNA-seq and Ribo-seq data**
+4. (default, optional) Identify translated ORFs using P-site periodicity and read density ([`RiboCode`](https://github.com/zhengtaoxiao/RiboCode))
+5. (default, optional) Derive P-sites and QC from transcriptome alignments ([`riboWaltz`](https://github.com/LabTranslationalArchitectomics/riboWaltz))
+6. (optional) Use a translational efficiency approach to study the dynamics of transcription and translation, with [anota2seq](https://bioconductor.org/packages/release/bioc/html/anota2seq.html). **requires matched RNA-seq and Ribo-seq data**
 
 ## Usage
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -869,6 +869,43 @@ if (!params.skip_ribotricer) {
     }
 }
 
+if (!params.skip_ribocode) {
+    process {
+        withName: 'RIBOCODE_GTFUPDATE' {
+            ext.args   = { params.extra_ribocode_gtfupdate_args ?: '' }
+        }
+        withName: 'RIBOCODE_PREPARE' {
+            ext.args   = { params.extra_ribocode_prepare_args ?: '' }
+        }
+        withName: 'RIBOCODE_METAPLOTS' {
+            ext.args   = { params.extra_ribocode_metaplots_args ?: '' }
+            publishDir = [
+                path: { "${params.outdir}/riboseq_qc/ribocode" },
+                mode: params.publish_dir_mode,
+                pattern: "*.{pdf,txt}",
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+        withName: 'RIBOCODE_RIBOCODE' {
+            ext.args   = { params.extra_ribocode_ribocode_args ?: '' }
+            publishDir = [
+                [
+                    path: { "${params.outdir}/orf_predictions/ribocode" },
+                    mode: params.publish_dir_mode,
+                    pattern: "*.txt",
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ],
+                [
+                    path: { "${params.outdir}/riboseq_qc/ribocode" },
+                    mode: params.publish_dir_mode,
+                    pattern: "*.{pdf,hd5}",
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                ]
+            ]
+        }
+    }
+}
+
 if (!params.skip_ribowaltz) {
     process {
         withName: 'RIBOWALTZ' {

diff --git a/conf/test.config b/conf/test.config
@@ -31,5 +31,6 @@ params {
     min_trimmed_reads = 1000
 
     skip_ribotricer = true
+    skip_ribocode = true
     extra_fqlint_args = '--disable-validator P001 --disable-validator S007'
 }
diff --git a/docs/output.md b/docs/output.md
@@ -31,9 +31,11 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
   - [Riboseq-specific QC](#riboseq-specific-qc)
     - [Ribo-TISH quality](#ribo-tish-quality)
     - [Ribotricer detect-orfs QC outputs](#ribotricer-detect-orfs-qc-outputs)
+    - [RiboCode metaplots](#ribocode-metaplots)
   - [ORF predictions](#orf-predictions)
     - [Ribo-TISH predict](#ribo-tish-predict)
     - [Ribotricer detect-orfs](#ribotricer-detect-orfs)
+    - [RiboCode](#ribocode)
   - [P-site identification](#p-site-identification)
     - [riboWaltz](#ribowaltz)
   - [Quantification](#quantification)
@@ -314,6 +316,16 @@ Read distribution metrics around annotated protein coding regions or based on al
   - `*_metagene_profiles_3p.tsv`: Metagene profile aligning with the stop codon
   </details>
 
+### RiboCode metaplots
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `riboseq_qc/ribocode/`
+  - `*_config.txt`: Configuration file containing P-site offsets for different read lengths
+  - `*.pdf`: Metaplot showing read density around start and stop codons
+  </details>
+
 ## ORF predictions
 
 ### Ribo-TISH predict
@@ -341,6 +353,16 @@ Read distribution metrics around annotated protein coding regions or based on al
   - `*_psite_offsets.txt`: If the P-site offsets are not provided, txt file containing the derived relative offsets
   </details>
 
+### RiboCode
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `orf_predictions/ribocode/`
+  - `*.txt`: ORF predictions with coordinates, read counts, and translation scores
+  - `*_collapsed.txt`: Collapsed ORF predictions removing redundant isoforms
+  </details>
+
 ## P-site identification
 
 ### riboWaltz

diff --git a/modules.json b/modules.json
@@ -95,6 +95,26 @@
                         "git_sha": "9656d955b700a8707c4a67821ab056f8c1095675",
                         "installed_by": ["modules"]
                     },
+                    "ribocode/gtfupdate": {
+                        "branch": "master",
+                        "git_sha": "3b13c6d5817ba9611477a7aa37120d9a9e50fff0",
+                        "installed_by": ["modules"]
+                    },
+                    "ribocode/metaplots": {
+                        "branch": "master",
+                        "git_sha": "3b13c6d5817ba9611477a7aa37120d9a9e50fff0",
+                        "installed_by": ["modules"]
+                    },
+                    "ribocode/prepare": {
+                        "branch": "master",
+                        "git_sha": "3b13c6d5817ba9611477a7aa37120d9a9e50fff0",
+                        "installed_by": ["modules"]
+                    },
+                    "ribocode/ribocode": {
+                        "branch": "master",
+                        "git_sha": "3b13c6d5817ba9611477a7aa37120d9a9e50fff0",
+                        "installed_by": ["modules"]
+                    },
                     "ribodetector": {
                         "branch": "master",
                         "git_sha": "61ce58ac3e4e4627d9c1cdc958ee6bfa742a0a75",

diff --git a/modules/nf-core/ribocode/gtfupdate/environment.yml b/modules/nf-core/ribocode/gtfupdate/environment.yml
diff --git a/modules/nf-core/ribocode/gtfupdate/main.nf b/modules/nf-core/ribocode/gtfupdate/main.nf
diff --git a/modules/nf-core/ribocode/gtfupdate/meta.yml b/modules/nf-core/ribocode/gtfupdate/meta.yml
diff --git a/modules/nf-core/ribocode/gtfupdate/tests/main.nf.test b/modules/nf-core/ribocode/gtfupdate/tests/main.nf.test