Add DIAMOND blastp subworkflow for protein homology search against NCBI RefSeq

.gitignore

@@ -13,3 +13,4 @@ null/
 .nf-test/tests
 .nf-test-*.nf
 .nf-test/*
+.vscode/

CHANGELOG.md

@@ -28,6 +28,14 @@ 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)
 - [#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 +10,10 @@
 
 ## 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

@@ -40,6 +40,7 @@ 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.
    - ([`KOfamScan`](https://github.com/takaram/kofam_scan)) assigns KEGG Orthologs to protein sequences using profile HMMs and KO-specific score thresholds.
 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/))

conf/modules.config

@@ -146,6 +146,22 @@ process {
         ]
     }
 
+    withName: 'NFCORE_PROTEINANNOTATOR:PROTEINANNOTATOR:FUNCTIONAL_ANNOTATION:DIAMOND:DIAMOND_MAKEDB' {
+        publishDir = [
+            path: { "${params.outdir}/downloaded_dbs/diamond/" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: 'NFCORE_PROTEINANNOTATOR:PROTEINANNOTATOR:FUNCTIONAL_ANNOTATION:DIAMOND:DIAMOND_BLASTP' {
+        publishDir = [
+            path: { "${params.outdir}/functional_annotation/diamond/${meta.id}/" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: 'NFCORE_PROTEINANNOTATOR:PROTEINANNOTATOR:FUNCTIONAL_ANNOTATION:ARIA2_INTERPROSCAN' {
         publishDir = [
             path: { "${params.outdir}/downloaded_dbs/" },

conf/test.config

@@ -24,6 +24,11 @@ params {
 
     // Input data
     input = params.pipelines_testdata_base_path + 'proteinannotator/samplesheet/samplesheet.csv'
+    // Diamond
+    refseq_release    = 'other'
+    refseq_fasta_url  = params.pipelines_testdata_base_path + 'proteinannotator/testdata/diamond/refseq/release/other/other.wp_protein_test.1.protein.faa.gz'
+    taxondmp_zip      = params.pipelines_testdata_base_path + 'proteinannotator/testdata/diamond/mini_taxdump.tar.gz'
+    taxonmap          = params.pipelines_testdata_base_path + 'proteinannotator/testdata/diamond/mini_prot.accession2taxid.gz'
     // Domain annotation
     pfam_latest_link        = params.pipelines_testdata_base_path + 'proteinannotator/testdata/pfam/Pfam-A_test.hmm.gz'
     funfam_latest_link      = params.pipelines_testdata_base_path + 'proteinannotator/testdata/funfam/funfam-hmm3-v4_3_0_test.lib.gz'