feature: added BiG-SLiCE analysis tool to pipeline by andreassag · Pull Request #7 · andreassag/clystere

andreassag · 2026-04-25T14:32:06Z

Added tool BiG-SLiCE alongside BiG-SCAPE for clustering analysis of Antismash results.

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Pull request overview

Adds BiG-SLiCE as an alternative clustering step to BiG-SCAPE in the antiSMASH pipeline, including new module wiring, parameters, schema updates, and documentation.

Changes:

Introduce a new BIGSLICE Nextflow module and integrate it into the main workflow (mutually exclusive with BiG-SCAPE).
Rename --run_bigscape to --bigscape_run and add new --bigslice_* parameters across config + schema.
Update docs/README/citations to reflect BiG-SLiCE support and outputs.

Reviewed changes

Copilot reviewed 17 out of 17 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
workflows/clystere.nf	Adds BiG-SLiCE module inclusion, mutually-exclusive flag guard, and conditional BIGSLICE execution.
nextflow_schema.json	Renames BiG-SCAPE run flag, adds BiG-SLiCE option group, and enforces mutual exclusion in schema.
nextflow.config	Renames BiG-SCAPE run param, adds BiG-SLiCE params, bumps pipeline version.
modules/local/bigslice/main.nf	New BiG-SLiCE process implementation (models bootstrap + run + optional archive).
modules/local/bigslice/environment.yml	New conda environment definition for BiG-SLiCE.
modules/local/bigscape/environment.yml	Pins BiG-SCAPE conda version for reproducibility.
main.nf	Points main entry to `workflows/clystere`.
docs/usage.md	Documents running BiG-SCAPE with new flag name and adds BiG-SLiCE usage example.
docs/parameters.md	Documents renamed BiG-SCAPE flag and adds BiG-SLiCE parameter table + notes.
docs/output.md	Documents `bigslice/` output directory and updates BiG-SCAPE flag name.
docs/installation.md	Reformats container engine installation section (tabbed UI).
docs/index.md	Updates overview text and diagram to include BiG-SLiCE.
conf/test_full.config	Updates test profile param name for BiG-SCAPE run flag.
conf/test.config	Updates test profile param name for BiG-SCAPE run flag.
conf/modules.config	Adds BIGSLICE module `ext.args` + publishDir configuration.
README.md	Updates feature list, params, outputs, and citations section for BiG-SLiCE + renamed flag.
CITATIONS.md	Adds BiG-SLiCE citation entry.

Comments suppressed due to low confidence (1)

workflows/clystere.nf:92

This workflow is still exported as ANTISMASH_BIGSCAPE, but it now conditionally runs either BiG-SCAPE or BiG-SLiCE. Consider renaming it to a tool-agnostic name (or add a short comment explaining why the legacy name is kept) to reduce confusion for future maintenance.

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Copilot · 2026-04-25T14:37:38Z

+=== Apptainer

-Follow the [Apptainer installation guide](https://apptainer.org/docs/user/latest/quick_start.html). Verify with
-`apptainer --version`.
+    ```text
+    Follow the [Apptainer installation guide](https://apptainer.org/docs/user/latest/quick_start.html). Verify with
+    `apptainer --version`.
+    ```


MkDocs Material tabbed syntax requires quoted tab titles (e.g. === "Apptainer") and the tab body should not be wrapped in a text code fence unless you intentionally want to disable Markdown/link rendering. Adjust the tab markup so this section renders as intended.

Copilot · 2026-04-25T14:37:38Z

+=== Conda

-Install [Miniconda](https://docs.conda.io/en/latest/miniconda.html) or Mamba. All tool environments are managed
-per-process by Nextflow.
+    ```text
+    Install [Miniconda](https://docs.conda.io/en/latest/miniconda.html) or Mamba. All tool environments are managed
+    per-process by Nextflow.
+    ```


MkDocs Material tabbed blocks use === "Conda" (quoted) and indented Markdown content. The current === Conda + fenced text block likely breaks tab rendering and prevents links from rendering as links.

Copilot · 2026-04-25T14:37:39Z

  // BiG-SCAPE
  // ──────────────────────────────────────────────
-  run_bigscape = false
+  bigscape_run = false


Renaming run_bigscape to bigscape_run is a breaking CLI change (existing command lines using --run_bigscape will silently stop enabling BiG-SCAPE). Consider keeping run_bigscape as a deprecated alias (mapped to bigscape_run) and/or bumping the major pipeline version to reflect the breaking change.

Copilot · 2026-04-25T14:37:39Z

  description = 'Nextflow pipeline for antiSMASH + BiG-SCAPE BGC analysis'
  mainScript = 'main.nf'
  nextflowVersion = '!>=23.04.0'
-  version = '1.0.0'
+  version = '1.1.0'


The manifest description still only mentions BiG-SCAPE even though this release adds BiG-SLiCE. Update the description to reflect the new functionality; also consider whether the version bump is appropriate given the breaking --run_bigscape → --bigscape_run rename.

Copilot · 2026-04-25T14:37:39Z

    B --> E[BIGSCAPE<br/>GCF clustering]
+    B --> F[BIGSLICE<br/>GCF clustering]


The overview diagram shows both BIGSCAPE and BIGSLICE running from antiSMASH, but the pipeline enforces these options as mutually exclusive. Consider adjusting the Mermaid graph to communicate that only one of these clustering steps runs per execution (e.g., alternative branch/annotation).

Suggested change

B --> E[BIGSCAPE GCF clustering]

B --> F[BIGSLICE GCF clustering]

B --> G{Optional GCF clustering choose one}

G --> E[BIGSCAPE GCF clustering]

G --> F[BIGSLICE GCF clustering]

Copilot · 2026-04-25T14:37:39Z

+=== Docker

-Follow the [Docker installation guide](https://docs.docker.com/get-docker/). Verify with `docker --version`.
+    ```text
+    Follow the [Docker installation guide](https://docs.docker.com/get-docker/). Verify with `docker --version`.
+    ```


MkDocs Material tabbed syntax requires quoted tab titles (e.g. === "Docker") and the tab body can be normal Markdown. As written (=== Docker plus fenced text blocks), the tabs may not render and the links become non-clickable; update the syntax/indentation accordingly.

feature: added BiG-SLiCE analysis tool to pipeline

77eefca

Copilot AI review requested due to automatic review settings April 25, 2026 14:32

Copilot started reviewing on behalf of andreassag April 25, 2026 14:32 View session

andreassag merged commit 586a011 into main Apr 25, 2026
12 checks passed

andreassag deleted the release/1.1.0 branch April 25, 2026 14:34

Copilot AI reviewed Apr 25, 2026

View reviewed changes

-    B --> E[BIGSCAPE<br/>GCF clustering]
-    B --> F[BIGSLICE<br/>GCF clustering]
+    B --> G{Optional GCF clustering<br/>choose one}
+    G --> E[BIGSCAPE<br/>GCF clustering]
+    G --> F[BIGSLICE<br/>GCF clustering]

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feature: added BiG-SLiCE analysis tool to pipeline - #7

feature: added BiG-SLiCE analysis tool to pipeline#7
andreassag merged 1 commit into
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release/1.1.0

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		B --> E[BIGSCAPE<br/>GCF clustering]
		B --> F[BIGSLICE<br/>GCF clustering]

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