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/)

docs/CONTRIBUTING.md

@@ -182,4 +182,95 @@ If you update images or graphics, follow the nf-core [style guidelines](https://
 
 ## Pipeline specific contribution guidelines
 
-<!-- TODO nf-core: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc. -->
+### Pipeline specific conventions
+
+- [ ] Use `nextflow` autoformatter
+- [ ] Channel assingment with `=` NOT `.set`
+- [ ] Parameter names structure: `<pipelinesection>_<toolname>_<parameter>`
+  - All components of structure should not have `_`, i.e., they should all be concatenated: `amp_hmmsearch_savealignments` not `amp_hmmsearch_save_alignments`
+  - Exception: subworkflow specific activation parameters must start with 'run': `run_<pipelinesection>_screening`, e.g. `run_arg_screening`
+  - Execption: tool specific skipping parameters must use 'skip' in the second position: `<pipelinesection>_skip_<toolname>`, e.g. `amp_skip_macrel`
+
+### Adding new tool workflow
+
+This checklist covers adding a specific tool to an _existing_ screening subworkflow.
+
+> [!NOTE]
+> Does not have to be in this precise order
+
+- [ ] Installed modules `nf-core modules install <tool>/<subtool>`
+- [ ] Added tools(s) to relevant `subworkflows/local/<screentype>.nf`
+  - [ ] Added relevant modules at the top using `include` statement
+  - [ ] Added the tool-specific if/else statement controlled with `params.<screentype>_skip_<toolname>`
+  - [ ] (Old nf-core module template only) Version channels mixed for every newly module
+  - [ ] (If applicable) Include auto-database downloading module, if tool needs it
+  - [ ] (If applicable) Within if/else condition, output channels mixed into the subworkflow's final aggregation/summary tool mix output file for aggregating tool (e.g. hAMRronize, AMPcombi etc.)
+  - [ ] (If applicable) MultiQC channels mixed
+- [ ] Updated `workflows/funcscan.nf`
+  - [ ] (If applicable) Added new input files via dedicated input channel
+  - [ ] (If applicable) Added tool specific input control conditions within the screening subworkflow's if/else statement
+- [ ] Added parameters and defaults added to `nextflow.config`
+  - [ ] Added all new parameters following [pipeline-specific conventions](#pipeline-specific conventions)
+  - [ ] (If applicable) Where possible, include parameter for supplying locally-downloaded database
+- [ ] Update `modules.conf`
+  - [ ] Added `withName:` block
+  - [ ] Added `ext.args = {}` entry including relevant new pipeline parameters
+  - [ ] Added `publishDir` placing relevant output files into the screening-subworkflow specific directory with `"${params.outdir}/<screentype>/<toolname>/`
+- [ ] If necessary, added any additional pre-execution parameter validation checks at the top of `subworkflows/local/utils_nfcore_funcscan_pipeline.nf` (e.g. for mutually exclusive parameters)
+- [ ] Updated Documentation
+  - [ ] `nf-core pipelines schema build` has been run and updated
+    - [ ] Checked all tool-specific pipeline parameters moved to the relevant screen type section of schema
+    - [ ] Checked all tool-specific pipeline parameters have short help text
+    - [ ] (If appplicable) Checked all tool-specific pipeline parameters have validation checks added (e.g. number range, fixed list etc.)
+    - [ ] Checked all tool-specific pipeline parameters have long-description with more information, including pointing to original documentation of tool itself
+    - [ ] (If applicable) Checked all tool-specific pipeline parameters have the `Modifies tool parameter(s)` quote block
+  - [ ] Added citation to `CITATIONS.md` (citation style: APA 7th edition)
+  - [ ] Added citation to the toolCitation/BibliographyText functions in `subworkflows/local/utils_nfcore_funcscan_pipeline`
+    - [ ] Added in-text citation
+    - [ ] Added bibliography (citation style: APA 7th edition)
+  - [ ] Added relevant documentation to `usage.md`
+    - [ ] (If applicable) Added entry in 'Databases and reference files' on how to download databases manually
+    - [ ] (If applicable) Added entry in 'Notes on screening tools <...>' if specific guidance is needed for execution
+    - [ ] (If applicable) If new input sample input files (e.g. annotation files) required, updated samplesheet description
+  - [ ] Described module output in `output.md`
+    - [ ] Added entry in relevant screening subworkflow section in introduction
+    - [ ] Added entry in introduction `tree` of whole output directory
+    - [ ] Added entry in 'Pipeline overview' table of contents
+    - [ ] Added dedicated 'Tool details' section in relevant subworkflow section including collapsable output list, description of a tool, and (ideally) description what primary output files can be used for
+      - [ ] Checked all output files specified in the `pattern:` section of `publishDir` are listed if `pattern:` is used, otherwise just all files found in results directory
+  - [ ] Added entry to 'Pipeline summary list' on `README.md`
+  - [ ] (Optional) Added to pipeline metro map diagram (can be done just before release)
+  - [ ] (First time contributor) add or move yourself to the Team list on `README.md`!
+  - [ ] (First time contributor) add or move yourself to the manifest section of `nextflow.config` as `contributor`
+- [ ] (If applicable) On nf-core/test-data: added small test-database on the [funcscan](https://github.com/nf-core/test-datasets/tree/funcscan) branch
+  - [ ] Added documentation of source and/or how test-data generated/modified
+- Updated relevant `conf/test*.conf`
+  - Specified skipping new tool to `true` in `test_minimal.config`
+  - (If applicable) Included/adjusted parameters in all relevant test configs
+  - (If applicable) Added paths to new test database files
+- Updated tests
+  - Added assertions to all output files for each test the tool is executed in
+  - Updated relevant snapshots with `nf-test --tag <tag> --profile +<docker,conda/apptainer> --update-snapshot`
+  - Checked assertions stable with `nf-test --tag <tag> --profile +<docker,conda/apptainer>`
+- Added entry to `CHANGELOG.md` (note: PR number can be added after)
+  - Tagged issue reporter/feature requester as well as author of PR
+
+### Adding a new screening subworkflow workflow
+
+Screening subworkflows should
+
+- [ ] Be written as a local subworkflow
+- [ ] By default run all tools, and offer skipping of execution
+- [ ] Include final emit channels at a minimum including:
+  - [ ] Versions channel
+  - [ ] (If any tools supported) MultiQC channel
+  - [ ] (If aggregation tool exists) include an aggregation tool step
+
+Subworkflows within the primary `workflow/funcscan.nf` file, should
+
+- [ ] Should be imported at the top of the module
+- [ ] Have a dedicated if/else statement with running with and without taxonomic classification
+  - [ ] Should include a empty file filter
+  - [ ] (If subworkflow includes tools using old nf-core/modules structure) Should include the versions mixing
+- [ ] (If applicable) be added to the Annotation if/else statement
+- [ ] (If applicable) be included in the MultiQC annotation if/else statement