[ch99l]

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[Copilot]

Pull request overview

This PR updates the pipeline to a newer bambu API/container and refreshes GitHub Actions workflows to support building/publishing the R container and controlling CI concurrency.

Changes:

• Update bambu.singlecell(...) calls to the newer output=...-driven API and adjust inputs/outputs accordingly (including removing sample_names plumbing).
• Simplify Seurat clustering outputs to a single clusters.rds mapping and remove unused R dependencies (IRanges).
• Pin the R container to ghcr.io/goekelab/bambu-pipe-r:1.0.0, switch the Docker build to a newer bambu branch, add a container build workflow, and update smoke-test workflow triggers/concurrency.

Reviewed changes

Copilot reviewed 11 out of 11 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
subworkflows/clustering.nf	Removes sample_names input and updates multi-sample Seurat invocation accordingly.
modules/seurat/single_sample.nf	Removes IRanges, changes how clusters are stored/exported from Seurat.
modules/seurat/multi_sample.nf	Removes IRanges and sample_names input; changes cluster labeling/export format.
modules/bambu/transcript_discovery.nf	Updates bambu calls to new API, removes sample_names emission, adjusts read/quant outputs.
modules/bambu/EM_quant.nf	Updates clustered EM invocation to pass reads=quantData and use new output modes.
modules/bambu/construct_read_class.nf	Updates read-class construction to new bambu API (output="readClasses").
main.nf	Updates CLUSTERING wiring to match removed sample_names output.
containers/r/Dockerfile	Switches bambu git branch used during container build.
conf/containers.config	Pins the R container image/tag to ghcr.io/goekelab/bambu-pipe-r:1.0.0.
.github/workflows/smoke_test.yml	Adds concurrency + workflow_dispatch; removes push trigger (see comment).
.github/workflows/build_container.yml	Adds workflow to build/publish the R container tag derived from conf/containers.config.

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