Add DIAMOND blastp subworkflow for protein homology search against NCBI RefSeq

.gitignore

@@ -12,4 +12,4 @@ null/
 .nf-test.log
 .nf-test/tests
 .nf-test-*.nf
-.nf-test/*
+.nf-test/*

.nf-test.log

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+Apr-09 11:11:33.550 [main] INFO  com.askimed.nf.test.App - nf-test 0.9.4
+Apr-09 11:11:33.572 [main] INFO  com.askimed.nf.test.App - Arguments: [test, subworkflows/local/domain_annotation, --profile, test,docker, --update-snapshot, --tag, stub]
+Apr-09 11:11:34.489 [main] INFO  com.askimed.nf.test.App - Nextflow Version: 25.10.4
+Apr-09 11:11:34.491 [main] INFO  com.askimed.nf.test.commands.RunTestsCommand - Load config from file /home/trace/projects/proteinannotator/nf-test.config...
+Apr-09 11:11:35.532 [main] INFO  com.askimed.nf.test.lang.dependencies.DependencyResolver - Loaded 37 files from directory /home/trace/projects/proteinannotator in 0.188 sec
+Apr-09 11:11:35.535 [main] INFO  com.askimed.nf.test.lang.dependencies.DependencyResolver - Found 1 files containing tests.
+Apr-09 11:11:35.535 [main] DEBUG com.askimed.nf.test.lang.dependencies.DependencyResolver - Found files: [/home/trace/projects/proteinannotator/subworkflows/local/domain_annotation/tests/main.nf.test]
+Apr-09 11:11:35.960 [main] INFO  com.askimed.nf.test.commands.RunTestsCommand - Found 0 tests to execute.

.vscode/settings.json

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 {
-    "markdown.styles": ["public/vscode_markdown.css"]
+    "markdown.styles": [
+        "public/vscode_markdown.css"
+    ],
+    "nextflow.telemetry.enabled": true
 }

CHANGELOG.md

@@ -7,6 +7,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `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 #50](https://github.com/nf-core/proteinannotator/pull/50)] Add DIAMOND subworkflow to run [Diamond](https://github.com/bbuchfink/diamond)
+- [[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
+- [#90](https://github.com/nf-core/proteinannotator/pull/90) - Added the option to download and use the latest `metagRoot` HMM library (or use path to an existing one) for domain annotation. (by @angelphanth)
 - [#90](https://github.com/nf-core/proteinannotator/pull/90) - Added the option to download and use the latest `metagRoot` HMM library (or use path to an existing one) for domain annotation. (by @angelphanth)
 - [#87](https://github.com/nf-core/proteinannotator/pull/87) - Added the option to download and use the latest `NMPFams` HMM library (or use path to an existing one) for domain annotation. (by @npechl)
 - [#85](https://github.com/nf-core/proteinannotator/pull/85) - Added zenodo doi in `nextflow.config`. (by @vagkaratzas)

CITATIONS.md

@@ -10,6 +10,11 @@
 
 ## Pipeline tools
 
+
+- [DIAMOND](https://github.com/bbuchfink/diamond)
+
+> Buchfink B, Xie C, Huson DH, "Fast and sensitive protein alignment using DIAMOND", Nature Methods 12, 59-60 (2015). doi:10.1038/nmeth.3176
+
 - [SeqFu](https://pubmed.ncbi.nlm.nih.gov/34066939/)
 
 > Telatin A, Fariselli P, Birolo G. SeqFu: a suite of utilities for the robust and reproducible manipulation of sequence files. Bioengineering. 2021 May 7;8(5):59. doi: 10.3390/bioengineering8050059. PubMed PMID: 34066939; PubMed Central PMCID: PMC8148589.

README.md

@@ -23,6 +23,14 @@
 
 **nf-core/proteinannotator** is a bioinformatics pipeline that computes statistics for protein FASTA inputs and produces protein annotations based on predicted sequence features, including conserved domains, functions, and secondary structure.
 
+1. Run ([`seqkit stats`](https://bioinf.shenwei.me/seqkit/usage/#stats)) to summarize input protein fasta files
+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.
+   2. ([`DIAMOND`](https://github.com/bbuchfink/diamond)) tool used for sensitive protein sequence alignment, comparing to a reference database created from combined protein fastas and taxonic information (taxon names, nodes, and map).
+3. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+
+
+<h1>
 <p>
   <picture>
     <source media="(prefers-color-scheme: dark)" srcset="docs/images/proteinannotator_metromap_dark.png">
@@ -40,6 +48,7 @@ Generate input amino acid sequence statistics with ([`SeqFu`](https://github.com
    such as [Pfam](https://ftp.ebi.ac.uk/pub/databases/Pfam/), [FunFam](https://download.cathdb.info/cath/releases/all-releases/), and [NMPFams and metagRoot](https://pavlopoulos-lab.org/envofams/databases/hmmer/)
 2. Functional annotation:
    - ([`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.
+   - ([`DIAMOND`](https://github.com/bbuchfink/diamond)) a rapid and sensitive protein sequence aligner used to search input sequences against a reference database built from NCBI RefSeq protein sequences with taxonomic information, providing potential homologous protein matches across species.
 3. Predict secondary structure compositional features such as α-helices, β-strands and coils with ([`s4pred`](https://github.com/psipred/s4pred))
 4. Present QC stats for input sequences before and after initial pre-processing with ([`MultiQC`](http://multiqc.info/))