v0.9.1 update

Author: ch99l

.github/workflows/smoke_test.yml

@@ -0,0 +1,42 @@
+name: Smoke Tests
+
+on:
+  push:
+    branches: [main, devel]
+  pull_request:
+    branches: [main, devel]
+
+jobs:
+  smoke_test:
+    name: "${{ matrix.profile }} (NF ${{ matrix.nextflow_version }})${{ matrix.quantification_mode && format(' [{0}]', matrix.quantification_mode) || '' }}${{ matrix.bam_only && ' [bam_only]' || '' }}"
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        include:
+          # Nextflow 26.04.0 - all profiles
+          - {nextflow_version: "26.04.0", profile: test_sc_fastq}
+          - {nextflow_version: "26.04.0", profile: test_sc_bam}
+          - {nextflow_version: "26.04.0", profile: test_sc_multi}
+          - {nextflow_version: "26.04.0", profile: test_visium}
+          - {nextflow_version: "26.04.0", profile: test_custom}
+          # latest-stable - all profiles (default EM_clusters)
+          - {nextflow_version: "latest-stable", profile: test_sc_fastq}
+          - {nextflow_version: "latest-stable", profile: test_sc_bam}
+          - {nextflow_version: "latest-stable", profile: test_sc_multi}
+          - {nextflow_version: "latest-stable", profile: test_visium}
+          - {nextflow_version: "latest-stable", profile: test_custom}
+          # latest-stable - extra parameter variants
+          - {nextflow_version: "latest-stable", profile: test_sc_fastq, quantification_mode: EM}
+          - {nextflow_version: "latest-stable", profile: test_sc_multi, quantification_mode: EM}
+          - {nextflow_version: "latest-stable", profile: test_sc_fastq, quantification_mode: no_quant}
+          - {nextflow_version: "latest-stable", profile: test_sc_fastq, bam_only: true}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: nf-core/setup-nextflow@v2
+        with:
+          version: ${{ matrix.nextflow_version }}
+      - name: Run ${{ matrix.profile }}
+        run: |
+          nextflow run . -profile test_base,${{ matrix.profile }},docker \
+            ${{ matrix.quantification_mode && format('--quantification_mode {0}', matrix.quantification_mode) || '' }} \
+            ${{ matrix.bam_only && '--bam_only' || '' }}

.gitignore

@@ -1,4 +1,5 @@
 .claude/
+CLAUDE.md
 .smoke_test/
 .nextflow/
 .nextflow.log*

CHANGELOG.md

@@ -4,6 +4,16 @@ This file contains all notable changes to Bambu-Pipe.
 
 ---
 
+## [v0.9.1] - 2026-05-20
+
+### Added
+- Harmony batch correction for multi-sample Seurat clustering
+- Processing of CB/UB tagged custom BAM files
+- GitHub Actions workflow to run smoke test on push and pull request to `main` and `devel` branches
+
+### Changed
+- Upgraded pipeline to support Nextflow version `26.04.0` and above
+
 ## [v0.9-beta] - 2026-05-11
 
 ### Added
@@ -25,7 +35,7 @@ This file contains all notable changes to Bambu-Pipe.
 - `quantification_mode` parameter to control quantification strategy (`no_quant`, `EM`, `EM_clusters`)
 - Seurat clustering as a dedicated process (`SEURAT_CLUSTERING`) for cluster-based EM quantification
 - Joint clustering across all samples on a combined gene counts matrix (previously per-sample)
-- Cluster output restructured to an ordered list of `CompressedCharacterList`s, one per sample in `quantData` order (previously a flat single CCL mixing all samples)
+- Cluster output restructured to an ordered list of `CompressedCharacterList`, one per sample in `quantData` order (previously a flat single CCL mixing all samples)
 - `SEURAT_CLUSTERING` now takes gene counts matrix and sample names as inputs instead of the full `quantData` object
 - `clusterCells` helper inlined into the process (previously sourced from `bin/utilityFunctions.R`)
 - `early_stop_stage` parameter to terminate the pipeline after BAM or RDS generation

README.md

@@ -4,13 +4,14 @@ params {
     valid_chemistries           = ['10x3v2', '10x3v3', '10x3v4', '10x5v2', '10x5v3', 'visium-v1', 'visium-v2', 'visium-v3', 'visium-v4', 'visium-v5']
     valid_technologies          = ['ONT', 'PacBio']
     valid_quantification_modes  = ['no_quant', 'EM', 'EM_clusters']
-    valid_early_stop_stages     = ['rds', 'bam', null]
     save_intermediates          = false
     qfilter_threshold           = 10
     flexiplex_f_5prime          = 8
     flexiplex_f_3prime          = 13
     flexiplex_e                 = 1
     process_by_chromosome       = true
+    seurat_dim_single           = 15
+    seurat_dim_multi            = 30
     fusion_mode                 = false
     jaffal_ref_dir              = null
     jaffal_code_dir             = "$projectDir/jaffal"

conf/dev.config

@@ -20,36 +20,43 @@ profiles {
         }
         workDir = "${projectDir}/.smoke_test/work"
         params {
-            genome     = "${projectDir}/examples/GRCh38.primary_assembly.genome.chr9_1_1000000.fa"
-            annotation = "${projectDir}/examples/gencode.v49.primary_assembly.annotation.chr9_1_1000000.gtf"
+            genome     = "${projectDir}/examples/GRCh38.primary_assembly.genome.chr21.fa.gz"
+            annotation = "${projectDir}/examples/gencode.v49.primary_assembly.annotation.chr21.gtf.gz"
         }
     }
 
-    test_fastq {
+    test_sc_fastq {
         params {
-            input      = "${projectDir}/examples/samplesheet_test_fastq.csv"
-            output_dir = "${projectDir}/.smoke_test/test_fastq/output"
+            input      = "${projectDir}/examples/samplesheet_test_sc_fastq.csv"
+            output_dir = "${projectDir}/.smoke_test/test_sc_fastq/output"
         }
     }
 
-    test_bam {
+    test_sc_bam {
         params {
-            input      = "${projectDir}/examples/samplesheet_test_bam.csv"
-            output_dir = "${projectDir}/.smoke_test/test_bam/output"
+            input      = "${projectDir}/examples/samplesheet_test_sc_bam.csv"
+            output_dir = "${projectDir}/.smoke_test/test_sc_bam/output"
         }
     }
 
-    test_rds {
+    test_sc_multi {
         params {
-            input      = "${projectDir}/examples/samplesheet_test_rds.csv"
-            output_dir = "${projectDir}/.smoke_test/test_rds/output"
+            input      = "${projectDir}/examples/samplesheet_test_sc_multi.csv"
+            output_dir = "${projectDir}/.smoke_test/test_sc_multi/output"
         }
     }
 
-    test_multi {
+    test_visium {
         params {
-            input      = "${projectDir}/examples/samplesheet_test_multi.csv"
-            output_dir = "${projectDir}/.smoke_test/test_multi/output"
+            input      = "${projectDir}/examples/samplesheet_test_visium.csv"
+            output_dir = "${projectDir}/.smoke_test/test_visium/output"
+        }
+    }
+
+    test_custom {
+        params {
+            input      = "${projectDir}/examples/samplesheet_test_custom.csv"
+            output_dir = "${projectDir}/.smoke_test/test_custom/output"
         }
     }
 

conf/smoke_test.config

@@ -13,6 +13,7 @@ RUN micromamba install -y -n base -c conda-forge -c bioconda \
     r-biocmanager=1.30.27 \
     bioconductor-bambu=3.12.1 \
     r-seurat=5.4.0 \
+    r-harmony=2.0.2 \
     gxx=15.2.0 \
     && micromamba clean --all --yes