Add ribocode to workflow mimicking ribotricer implementation

CHANGELOG.md

@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#128](https://github.com/nf-core/riboseq/pull/128) - Add DESeq2-based deltaTE analysis as an alternative to anota2seq for translational efficiency analysis ([@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))
 - [#135](https://github.com/nf-core/riboseq/pull/135) - Add optional read length equalisation to trim RNA-seq reads to match Ribo-seq lengths before quantification ([@pinin4fjords](https://github.com/pinin4fjords))
+- [#136](https://github.com/nf-core/riboseq/pull/136) - Add RiboCode ORF detection with P-site analysis and metaplots ([@JackCurragh](https://github.com/JackCurragh))
 - [#138](https://github.com/nf-core/riboseq/pull/138) - Add MultiQC configuration for BBSplit, Bowtie2 rRNA removal, UMItools, and UMIcollapse ([@pinin4fjords](https://github.com/pinin4fjords))
 - [#140](https://github.com/nf-core/riboseq/pull/140) - Add P-site identification using plastid ([@suhrig](https://github.com/suhrig))
 
@@ -27,6 +28,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | 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`         |
 |               | `--translational_efficiency_method`      |
 |               | `--extra_deltate_args`                   |
 |               | `--te_lfc_threshold`                     |

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.

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), [`plastid`](https://plastid.readthedocs.io/en/latest/index.html))
-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), [`plastid`](https://plastid.readthedocs.io/en/latest/index.html))
+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
 

conf/modules.config

@@ -969,6 +969,43 @@ 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' {

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'
 }

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)
     - [plastid](#plastid)
@@ -315,6 +317,16 @@ 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
@@ -342,6 +354,16 @@ 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

modules.json

@@ -110,6 +110,26 @@
                         "git_sha": "8d66ebdfc2e09f449c03dcb3a08a9ee13f0412d3",
                         "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",