Add Interproscan

.github/actions/nf-test/action.yml

@@ -19,6 +19,18 @@ inputs:
 runs:
   using: "composite"
   steps:
+    - name: Print Modules Folder Tree
+      uses: jaywcjlove/github-action-folder-tree@main
+      with:
+        exclude: "node_modules|dist|.git|.husky"
+        path: ./modules
+        depth: 10
+    - name: Print Subworkflows Folder Tree
+      uses: jaywcjlove/github-action-folder-tree@main
+      with:
+        exclude: "node_modules|dist|.git|.husky"
+        path: ./subworkflows
+        depth: 10
     - name: Setup Nextflow
       uses: nf-core/setup-nextflow@v2
       with:

.github/workflows/nf-test.yml

@@ -25,6 +25,8 @@ concurrency:
 
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  NFT_DIFF: "pdiff"
+  NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
   NFT_VER: "0.9.2"
   NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
@@ -58,6 +60,7 @@ jobs:
           NFT_VER: ${{ env.NFT_VER }}
         with:
           max_shards: 7
+          tags: CI
 
       - name: debug
         run: |
@@ -106,6 +109,7 @@ jobs:
           profile: ${{ matrix.profile }}
           shard: ${{ matrix.shard }}
           total_shards: ${{ env.TOTAL_SHARDS }}
+          tags: CI
   confirm-pass:
     needs: [nf-test]
     if: always()

.gitignore

@@ -8,6 +8,8 @@ testing*
 *.pyc
 null/
 
-.nf-test/*
+# Nextflow nf-tests output
 .nf-test.log
-.nf-test-*
+.nf-test/tests
+.nf-test-*.nf
+.nf-test/*

.nf-core.yml

@@ -1,14 +1,16 @@
 lint:
   files_exist:
     - .github/workflows/ci.yml
+    - conf/igenomes.config
+    - conf/igenomes_ignored.config
+  actions_ci: false
   files_unchanged:
     - assets/nf-core-proteinannotator_logo_light.png
     - docs/images/nf-core-proteinannotator_logo_light.png
     - docs/images/nf-core-proteinannotator_logo_dark.png
     - .github/PULL_REQUEST_TEMPLATE.md
 nf_core_version: 3.3.1
 repository_type: pipeline
-
 template:
   author: Olga Botvinnik
   description: The best protein annotation pipeline in the world. Protein fasta ->

.prettierignore

@@ -11,3 +11,6 @@ testing*
 *.pyc
 bin/
 ro-crate-metadata.json
+**/Makefile
+Makefile
+modules/local/interproscan/tests/fixtures/interproscan_db/data

CHANGELOG.md

@@ -9,8 +9,13 @@ Initial release of nf-core/proteinannotator, created with the [nf-core](https://
 
 ### `Added`
 
+- [[PR #52](https://github.com/nf-core/proteinannotator/pull/52)] Add option to turn off InterProScan for testing
+- [[PR #51](https://github.com/nf-core/proteinannotator/pull/51)] Update to nf-core/tools v3.3.1
+- [[PR #47](https://github.com/nf-core/proteinannotator/pull/47)] Update metromap with more tools added from [May 2025 Hackathon](https://nf-co.re/events/2025/hackathon-boston)
+- [[PR #43](https://github.com/nf-core/proteinannotator/pull/44)] Add [mTM-Align](https://nf-co.re/modules/mtmalign_align/) and [MMseqs2 Search](https://nf-co.re/modules/mmseqs_search/) modules
 - [[PR #42](https://github.com/nf-core/proteinannotator/pull/42)] Updated to `nf-test` on GitHub Actions and in the `PULL_REQUEST_TEMPLATE.md`
 - [[PR #13](https://github.com/nf-core/proteinannotator/pull/13)] Add nf-core seqkit/stats module
+- [[PR #9](https://github.com/nf-core/proteinannotator/pull/9)] Add [InterProScan](https://interproscan-docs.readthedocs.io/) module
 
 ### `Fixed`
 

CITATIONS.md

@@ -14,6 +14,18 @@
 
 > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
+- [InterProScan](https://academic.oup.com/bioinformatics/article/17/9/847/206564)
+
+> 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.
+
+- [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.
+
+- [mTM-align](https://academic.oup.com/bioinformatics/article/34/10/1719/4769500)
+
+> Dong, Runze, Zhenling Peng, Yang Zhang, and Jianyi Yang. “mTM-Align: An Algorithm for Fast and Accurate Multiple Protein Structure Alignment.” Bioinformatics 34, no. 10 (May 15, 2018): 1719–25. https://doi.org/10.1093/bioinformatics/btx828.
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)

README.md

@@ -20,7 +20,7 @@
 
 ## Introduction
 
-**nf-core/proteinannotator** is a bioinformatics pipeline that ...
+**nf-core/proteinannotator** is a bioinformatics pipeline that runs statistics of input protein fasta files and identifies the function of proteins based on their sequence data, using state-of-the-art protein annotation tools such as [InterProScan](https://interproscan-docs.readthedocs.io/).
 
 <!-- TODO nf-core:
    Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the
@@ -34,7 +34,9 @@
 <!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
 
 1. Run ([`seqkit stats`](https://bioinf.shenwei.me/seqkit/usage/#stats)) to summarize input protein fasta files
-2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+2. Functional Annotation:
+   1. ([`InterProScan`](https://interproscan-docs.readthedocs.io/en/v5/)) a software tool used to analyze protein sequences by scanning them against the signatures of protein families, domains, and sites in the [InterPro](https://www.ebi.ac.uk/interpro/) database, helping to identify their functional characteristics.
+3. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 
 ![Protein annotator metromap. Protein fasta files are summarized with `seqkit stats`, then functionally annotated with InterProScan, DIAMOND-blastp, UniFire, and Kmerseek](assets/proteinannotator-metromap.excalidraw.png)
 

conf/test.config

@@ -14,18 +14,19 @@ process {
     resourceLimits = [
         cpus: 4,
         memory: '15.GB',
-        time: '1.h'
+        time: '1.h',
     ]
 }
 
 params {
-    config_profile_name        = 'Test profile'
+    config_profile_name = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Input data
     // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
     // From: https://github.com/nf-core/proteinfold/blob/1.1.1/conf/test.config
     // Example: https://github.com/nf-core/test-datasets/blob/proteinfold/testdata/samplesheet/v1.2/samplesheet.csv
-    input           = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.2/samplesheet.csv'
+    input = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.2/samplesheet.csv'
+    skip_interproscan = true
 }

conf/test_full.config

@@ -11,14 +11,11 @@
 */
 
 params {
-    config_profile_name        = 'Full test profile'
+    config_profile_name = 'Full test profile'
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
     // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
-
-    // Fasta references
-    fasta = params.pipelines_testdata_base_path + 'viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz'
+    input = params.pipelines_testdata_base_path + 'proteinannotator/samplesheet/snap25-isoforms.csv'
 }