Plastid

CHANGELOG.md

@@ -10,6 +10,7 @@ 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))
 - [#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))
+- [#134](https://github.com/nf-core/riboseq/pull/134) - Add P-site identification using plastid ([@suhrig](https://github.com/suhrig))
 
 ### `Fixed`
 
@@ -21,20 +22,28 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Parameters`
 
-| Old parameter | New parameter                       |
-| ------------- | ----------------------------------- |
-|               | `--ribo_removal_tool`               |
-|               | `--translational_efficiency_method` |
-|               | `--extra_deltate_args`              |
-|               | `--te_lfc_threshold`                |
-|               | `--rna_lfc_threshold`               |
-|               | `--ribo_lfc_threshold`              |
+| Old parameter | New parameter                            |
+| ------------- | ---------------------------------------- |
+|               | `--ribo_removal_tool`                    |
+|               | `--translational_efficiency_method`      |
+|               | `--extra_deltate_args`                   |
+|               | `--te_lfc_threshold`                     |
+|               | `--rna_lfc_threshold`                    |
+|               | `--ribo_lfc_threshold`                   |
+|               | `--skip_plastid`                         |
+|               | `--plastid_min_length`                   |
+|               | `--plastid_max_length`                   |
+|               | `--plastid_default_psite_offset`         |
+|               | `--extra_plastid_metagene_generate_args` |
+|               | `--extra_plastid_psite_args`             |
+|               | `--extra_plastid_make_wiggle_args`       |
 
 ### `Dependencies`
 
 | Dependency | Old version | New version |
 | ---------- | ----------- | ----------- |
 | `MultiQC`  | 1.32        | 1.33        |
+| `plastid`  |             | 0.6.1       |
 
 ## v1.2.0 - 2025-12-03
 

README.md

@@ -41,7 +41,7 @@ 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))
+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**
 
 ## Usage

conf/modules.config

@@ -887,6 +887,33 @@ if (!params.skip_ribowaltz) {
     }
 }
 
+if (!params.skip_plastid) {
+    process {
+        withName: 'PLASTID_METAGENE_GENERATE' {
+            ext.args = { [
+                params.extra_plastid_metagene_generate_args ?: '',
+                '--landmark cds_start'
+            ].join(' ').trim() }
+        }
+        withName: 'PLASTID_PSITE' {
+            ext.args = { [
+                params.extra_plastid_psite_args ?: '',
+                params.plastid_min_length ? "--min_length ${params.plastid_min_length}" : '',
+                params.plastid_max_length ? "--max_length ${params.plastid_max_length}" : '',
+                params.plastid_default_psite_offset ? "--default ${params.plastid_default_psite_offset}" : '',
+                '--require_upstream',
+            ].join(' ').trim() }
+        }
+        withName: 'PLASTID_MAKE_WIGGLE' {
+            ext.args = { [
+                params.extra_plastid_make_wiggle_args ?: '',
+                params.plastid_min_length ? "--min_length ${params.plastid_min_length}" : '',
+                '--output_format bedgraph'
+            ].join(' ').trim() }
+        }
+    }
+}
+
 if (params.contrasts) {
     process {
         withName: 'ANOTA2SEQ_ANOTA2SEQRUN' {

docs/output.md

@@ -36,6 +36,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
     - [Ribotricer detect-orfs](#ribotricer-detect-orfs)
   - [P-site identification](#p-site-identification)
     - [riboWaltz](#ribowaltz)
+    - [plastid](#plastid)
   - [Quantification](#quantification)
   - [Translational efficiency](#translational-efficiency)
     - [MultiQC](#multiqc)
@@ -372,6 +373,19 @@ P-sites are identified by passing transcriptome-level alignment BAM files to rib
 
   </details>
 
+P-sites are identified by passing genome-level alignment BAM files to plastid, producing the following outputs:
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `plastid/`
+  - `*.filtered_rois.bed` and `*.filtered_rois.txt`: Position of CDS start for each gene in BED or TXT format; used for metagene analysis
+  - `*_metagene_profiles.txt`: Matrix containing the distances of the 5' read ends to the CDS start position for each read length
+  - `*_p_offsets.png`: Graphical illustrations of the metagene profiles
+  - `*_p_offsets.txt`: Selected Optimal p-site offset for each read length
+
+  </details>
+
 ## Quantification
 
 Quantification is done by passing transcriptome-level alignment BAM files to Salmon, producing the following outputs:

docs/usage.md

@@ -240,6 +240,8 @@ The pipeline will by default run the [Ribo-TISH](https://github.com/zhpn1024/rib
 
 The pipeline will by default run [riboWaltz](https://github.com/LabTranslationalArchitectomics/riboWaltz) for P-site identification and diagnostics, unless disabled with `--skip_ribowaltz`. Additional arguments can be supplied via `--extra_ribowaltz_args` parameters. An example is: `--extra_ribowaltz_args "--length_range 27:31 --periodicity_threshold 40 --extremity 5end --start_nts 45 --stop_nts 24"`. If not provided, defaults used in the [nf-core module](https://github.com/nf-core/modules/blob/master/modules/nf-core/ribowaltz/templates/ribowaltz.r) are used.
 
+In addition, the pipeline runs [plastid](https://plastid.readthedocs.io/en/latest/index.html) to identify P-sites and create bedGraph tracks, unless disabled with `--skip_plastid`.
+
 ## Translational efficiency
 
 If you have paired RNA-seq and Riboseq samples, you can use this workflow to initiate a translational efficiency analysis.

modules.json

@@ -95,6 +95,21 @@
                         "git_sha": "9656d955b700a8707c4a67821ab056f8c1095675",
                         "installed_by": ["modules"]
                     },
+                    "plastid/make_wiggle": {
+                        "branch": "master",
+                        "git_sha": "8d66ebdfc2e09f449c03dcb3a08a9ee13f0412d3",
+                        "installed_by": ["modules"]
+                    },
+                    "plastid/metagene_generate": {
+                        "branch": "master",
+                        "git_sha": "8d66ebdfc2e09f449c03dcb3a08a9ee13f0412d3",
+                        "installed_by": ["modules"]
+                    },
+                    "plastid/psite": {
+                        "branch": "master",
+                        "git_sha": "8d66ebdfc2e09f449c03dcb3a08a9ee13f0412d3",
+                        "installed_by": ["modules"]
+                    },
                     "ribodetector": {
                         "branch": "master",
                         "git_sha": "61ce58ac3e4e4627d9c1cdc958ee6bfa742a0a75",