added s4pred module to pipeline

Author: vagkaratzas

CITATIONS.md

@@ -22,6 +22,10 @@
 
 > Zdobnov, Evgeni M., and Rolf Apweiler. “InterProScan – an Integration Platform for the Signature-Recognition Methods in InterPro.” Bioinformatics 17, no. 9 (September 1, 2001): 847–48. https://doi.org/10.1093/bioinformatics/17.9.847.
 
+- [s4pred](https://pubmed.ncbi.nlm.nih.gov/34213528/)
+
+> Moffat L, Jones DT. Increasing the accuracy of single sequence prediction methods using a deep semi-supervised learning framework. Bioinformatics. 2021 Nov 1;37(21):3744-51. doi: 10.1093/bioinformatics/btab491. PubMed PMID: 34213528; PubMed Central PMCID: PMC8570780.
+
 <!-- - [MMseqs2](https://www.nature.com/articles/nbt.3988)
 
 > Zdobnov, Evgeni M., and Rolf Apweiler. “InterProScan – an Integration Platform for the Signature-Recognition Methods in InterPro.” Bioinformatics 17, no. 9 (September 1, 2001): 847–48. https://doi.org/10.1093/bioinformatics/17.9.847.

conf/modules.config

@@ -74,6 +74,16 @@ process {
         ]
     }
 
+    withName: 'NFCORE_PROTEINANNOTATOR:PROTEINANNOTATOR:S4PRED_RUNMODEL' {
+        ext.prefix = { params.s4pred_outfmt }
+        ext.args   = { "--outfmt ${params.s4pred_outfmt}" }
+        publishDir = [
+            path: { "${params.outdir}/s4pred/${meta.id}/" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [

docs/output.md

@@ -18,6 +18,9 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 - [Functional Annotation](#functional-annotation) Annotate proteins with functional domains
   - [InterProScan](#Interproscan) - Search the InterPro database for functional domains
+
+- [s4pred](#s4pred) - Predict secondary structures of sequences, producing per amino acid probabilities of being an α-helix, a β-strand or a coil.
+
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
@@ -307,6 +310,22 @@ The XML Schema Definition (XSD) is available [here](http://ftp.ebi.ac.uk/pub/sof
 
 </details>
 
+#### s4pred
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `s4pred/`
+  - `<samplename>/`
+    - `<s4pred_outfmt>/`
+      - `<samplename>.<s4pred_outfmt>`: The probability of each amino acid to be an α-helix, a β-strand or a coil, in the chosen output format (i.e., 'ss2', 'fas', or 'horiz').
+
+</details>
+
+The `s4pred` module is used to predict secondary structures of amino acid sequences.
+
+[s4pred](https://github.com/psipred/s4pred) is a tool for accurate prediction of a protein's secondary structure from only it's amino acid sequence.
+
 ### MultiQC
 
 <details markdown="1">

modules.json

@@ -20,6 +20,11 @@
                         "git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49",
                         "installed_by": ["modules"]
                     },
+                    "s4pred/runmodel": {
+                        "branch": "master",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "installed_by": ["modules"]
+                    },
                     "seqfu/stats": {
                         "branch": "master",
                         "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",

modules/nf-core/s4pred/runmodel/environment.yml

@@ -24,6 +24,10 @@ params {
     interproscan_database = null
     interproscan_database_version = null
 
+    // Secondary structure prediction (s4pred)
+    skip_s4pred   = false
+    s4pred_outfmt = 'ss2'  // ["ss2", "fas", "horiz"]
+
     // MultiQC options
     multiqc_config = null
     multiqc_title = null