Add BiG-SLiCE to BGC workflow (fresh branch)

CHANGELOG.md

@@ -15,18 +15,21 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#507](https://github.com/nf-core/funcscan/pull/507) Updated to nf-core template v3.5.1 (by @jfy133)
 - [#510](https://github.com/nf-core funcscan/pull/510) Fixed code to make Nextflow strict-syntax compliant (by @jfy133)
 - [#521](https://github.com/nf-core funcscan/pull/521) Added option to turn on RGI's own cleanup of intermediate files (❤️ to @SamD28 for requesting, added by @jfy133)
+- [#519](https://github.com/nf-core/funcscan/pull/519) Added BiG-SLiCE (`bigslice`) as a new BGC clustering tool in the BGC subworkflow. Activated with `--bgc_run_bigslice` and requires `--bgc_bigslice_db`. (by @SkyLexS)
+- [#528](https://github.com/nf-core/funcscan/pull/528) Updated pipeline template to nf-core/tools version 4.0.2 (by @jfy133)
 
 ### `Fixed`
 
 - [#501](https://github.com/nf-core/funcscan/pull/501) Fixed issue with BAKTA HMMs not being staged correctly (reported by Yusuke Hioki, fix by @jfy133)
 
 ### `Dependencies`
 
-| Tool    | Previous Version | New Version |
-| ------- | ---------------- | ----------- |
-| dbCAN   |                  | 5.2.9       |
-| MultiQC | 1.27             | 1.34        |
-| Bakta   | 1.10.4           | 1.11.4      |
+| Tool      | Previous Version | New Version |
+| --------- | ---------------- | ----------- |
+| dbCAN     |                  | 5.2.9       |
+| MultiQC   | 1.27             | 1.34        |
+| Bakta     | 1.10.4           | 1.11.4      |
+| BiG-SLiCE |                  | 2.0.2       |
 
 ### `Deprecated`
 

CITATIONS.md

@@ -38,6 +38,12 @@
 
   > Schwengers, O., Jelonek, L., Dieckmann, M. A., Beyvers, S., Blom, J., & Goesmann, A. (2021). Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microbial Genomics, 7(11). [DOI: 10.1099/mgen.0.000685](https://doi.org/10.1099/mgen.0.000685)
 
+- [BiG-SLiCE](https://github.com/medema-group/bigslice)
+
+  > Kautsar, S. A., van der Hooft, J. J. J., de Ridder, D., & Medema, M. H. (2021). BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters. GigaScience, 10(1), giaa154. [DOI: 10.1093/gigascience/giaa154](https://doi.org/10.1093/gigascience/giaa154)
+
+  > Kautsar, S. A., et al. (2026). BiG-SLiCE 2.0: improved gene cluster family diversity mapping. Nature Communications. [DOI: 10.1038/s41467-026-68733-5](https://doi.org/10.1038/s41467-026-68733-5)
+
 - [comBGC](https://github.com/nf-core/funcscan)
 
   > Frangenberg, J., Fellows Yates, J. A., Ibrahim, A., Perelo, L., & Beber, M. E. (2023). nf-core/funcscan: 1.0.0 - German Rollmops - 2023-02-15. [DOI: 10.5281/zenodo.7643100](https://doi.org/10.5281/zenodo.7643099)

README.md

@@ -39,7 +39,7 @@ The nf-core/funcscan AWS full test dataset are contigs generated by the MGnify s
 4. Annotation of coding sequences from 3. to obtain general protein families and domains with [`InterProScan`](https://github.com/ebi-pf-team/interproscan)
 5. Screening contigs for antimicrobial peptide-like sequences with [`ampir`](https://cran.r-project.org/web/packages/ampir/index.html), [`Macrel`](https://github.com/BigDataBiology/macrel), [`HMMER`](http://hmmer.org/), [`AMPlify`](https://github.com/bcgsc/AMPlify)
 6. Screening contigs for antibiotic resistant gene-like sequences with [`ABRicate`](https://github.com/tseemann/abricate), [`AMRFinderPlus`](https://github.com/ncbi/amr), [`fARGene`](https://github.com/fannyhb/fargene), [`RGI`](https://card.mcmaster.ca/analyze/rgi), [`DeepARG`](https://bench.cs.vt.edu/deeparg). [`argNorm`](https://github.com/BigDataBiology/argNorm) is used to map the outputs of `DeepARG`, `AMRFinderPlus`, and `ABRicate` to the [`Antibiotic Resistance Ontology`](https://www.ebi.ac.uk/ols4/ontologies/aro) for consistent ARG classification terms.
-7. Screening contigs for biosynthetic gene cluster-like sequences with [`antiSMASH`](https://antismash.secondarymetabolites.org), [`DeepBGC`](https://github.com/Merck/deepbgc), [`GECCO`](https://gecco.embl.de/), [`HMMER`](http://hmmer.org/)
+7. Screening contigs for biosynthetic gene cluster-like sequences with [`antiSMASH`](https://antismash.secondarymetabolites.org), [`BiG-SLiCE`](https://github.com/medema-group/bigslice), [`DeepBGC`](https://github.com/Merck/deepbgc), [`GECCO`](https://gecco.embl.de/), [`HMMER`](http://hmmer.org/)
 8. Screening contigs for carbohydrate-active enzymes (CAZymes), CAZyme gene clusters and substrates with [run_dbcan](https://github.com/bcb-unl/run_dbcan).
 9. Creating aggregated reports for all samples across the workflows with [`AMPcombi`](https://github.com/paleobiotechnology/AMPcombi) for AMPs, [`hAMRonization`](https://github.com/pha4ge/hAMRonization) for ARGs, and [`comBGC`](https://raw.githubusercontent.com/nf-core/funcscan/master/bin/comBGC.py) for BGCs
 10. Software version and methods text reporting with [`MultiQC`](http://multiqc.info/)