Add BiG-SLiCE to BGC subworkflow

CHANGELOG.md

@@ -7,14 +7,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
-- [#483](https://github.com/nf-core/funcscan/pull/483) **New screening workflow** for CAZyme Gene Cluster (CGC) and substrate prediction, through dbCAN (by @HaidYi)
-- [#483](https://github.com/nf-core/funcscan/pull/483) Added support for preannotated input with optional GFF column in samplesheet for dbCAN CAZyme Gene Cluster (CGC) and substrate prediction, with new `--dbcan_skip_cgc` and `--dbcan_skip_substrate` parameters (by @HaidYi)
 - [#500](https://github.com/nf-core/funcscan/pull/500) Updated pipeline template to nf-core/tools version 3.4.1 (by @jfy133)
 - [#508](https://github.com/nf-core/funcscan/pull/508) Added support for antiSMASH's --clusterhmmer, --fullhmmer, and --tigrfam options (❤️ to @yusukepockyby for requesting, @jfy133)
 - [#506](https://github.com/nf-core/funcscan/pull/506) Added support GECCO convert for generation of additional files useful for downstream analysis (by @SkyLexS)
 - [#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. BiG-SLiCE clusters BGC sequences detected by antiSMASH and/or GECCO into Gene Cluster Families (GCFs) using an HMM-based approach. Activated with `--bgc_run_bigslice` and requires `--bgc_bigslice_db`. (by @SkyLexS)
 
 ### `Fixed`
 

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

@@ -39,10 +39,9 @@ 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/)
-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/)
+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. Creating aggregated reports for all samples across the workflows with [`AMPcombi`](https://github.com/Darcy220606/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
+9. Software version and methods text reporting with [`MultiQC`](http://multiqc.info/)
 
 ![funcscan metro workflow](docs/images/funcscan_metro_workflow.png)
 
@@ -93,7 +92,7 @@ nf-core/funcscan was originally written by Jasmin Frangenberg, Anan Ibrahim, Lou
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 
-Adam Talbot, Alexandru Mizeranschi, Haidong Yi, Hugo Tavares, Júlia Mir Pedrol, Martin Klapper, Mehrdad Jaberi, Robert Syme, Rosa Herbst, Vedanth Ramji, @Microbion, Dediu Octavian-Codrin.
+Adam Talbot, Alexandru Mizeranschi, Hugo Tavares, Júlia Mir Pedrol, Martin Klapper, Mehrdad Jaberi, Robert Syme, Rosa Herbst, Vedanth Ramji, @Microbion, Dediu Octavian-Codrin.
 
 ## Contributions and Support
 

conf/modules.config

@@ -541,6 +541,29 @@ process {
         ]
     }
 
+    withName: BIGSLICE {
+        errorStrategy = 'ignore'
+        ext.args   = [
+            params.bgc_bigslice_complete                  ? '--complete'                                                      : '',
+            params.bgc_bigslice_threshold     != 0.4   ? "--threshold ${params.bgc_bigslice_threshold}"                    : '',
+            params.bgc_bigslice_threshold_pct != 0.0   ? "--threshold_pct ${params.bgc_bigslice_threshold_pct}"             : '',
+            params.bgc_bigslice_n_ranks       != 1     ? "--n_ranks ${params.bgc_bigslice_n_ranks}"                        : ''
+        ].join(' ').trim()
+        publishDir = [
+            path: { "${params.outdir}/bgc/" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+
+    withName: BIGSLICE_DOWNLOADDB {
+        publishDir = [
+            path: { "${params.outdir}/bgc/bigslice_db" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+
     withName: HAMRONIZATION_ABRICATE {
         publishDir = [
             path: { "${params.outdir}/arg/hamronization/abricate" },