heylf · Oct 8, 2026 · Oct 6, 2026 · Oct 6, 2026 · Oct 8, 2026 · Oct 8, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,7 +9,7 @@ Initial release of nf-core/spatialaxe, created with the [nf-core](https://nf-co.
 
 ### `Added`
 
-- Added the entire **spoQC tool and subworkflow**: `subworkflows/local/spoqc/main.nf` plus 31 new local modules under `modules/local/spoQC/` (`ambient`, `analysis_category`, `analysis_cluster`, `analysis_overview`, `annotation`, `bubble`, `cell`, `cellcycle`, `combine_masks`, `doublet`, `finalreport`, `general`, `hqcr_celltype`, `hqcr_ident`, `hqpr_bounding_box`, `hqpr_celltype`, `hqpr_clustering`, `hqpr_metrices`, `hqpr_refinement`, `hqtr_ac`, `hqtr_bounding_box`, `hqtr_celltype`, `hqtr_clustering`, `hqtr_metrices`, `hqtr_qv`, `hqtr_refinement`, `marker`, `model`, `transcript`, `void`, `whole_slide`), each with its own `main.nf`, `meta.yml`, and nf-test suite (`tests/main.nf.test` + snapshot).
+- Added the entire **spoQC tool and subworkflow**: `subworkflows/local/spoqc/main.nf` plus 30 new local modules under `modules/local/spoQC/` (`ambient`, `analysis_category`, `analysis_cluster`, `analysis_overview`, `annotation`, `cell`, `cellcycle`, `combine_masks`, `doublet`, `finalreport`, `general`, `hqcr_celltype`, `hqcr_ident`, `hqpr_bounding_box`, `hqpr_celltype`, `hqpr_clustering`, `hqpr_metrices`, `hqpr_refinement`, `hqtr_ac`, `hqtr_bounding_box`, `hqtr_celltype`, `hqtr_clustering`, `hqtr_metrices`, `hqtr_qv`, `hqtr_refinement`, `marker`, `model`, `transcript`, `void`, `whole_slide`), each with its own `main.nf`, `meta.yml`, and nf-test suite (`tests/main.nf.test` + snapshot).
 - Wired spoQC into `workflows/spatialaxe.nf`.
 - Added `bin/spatialdata_write.py` support for spoQC's SpatialData output.
 - New test configs: `conf/tests/test_spoqc.config` and `conf/tests/test_full_spoqc.config`

diff --git a/conf/test.config b/conf/test.config
@@ -30,5 +30,7 @@ params {
 
     // Input data
     input                      = "${projectDir}/assets/samplesheet.csv"
-    mode                       = 'coordinate'
+    //mode                       = 'coordinate'
+    mode                       = 'qc'
+    spoqc                      = true
 }
diff --git a/docs/output.md b/docs/output.md
@@ -137,7 +137,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
       - `unsupervised_cell_annotation.tsv` unsupervised cell-type annotation, generated only when no annotation file was supplied as input
     - `whole_slide_qc/` whole-slide QC overview report
     - `generalqc/` general-purpose QC report
-    - `bubbleqc/` bubble-artifact QC report
     - `doubletqc/` doublet-detection QC report
     - `voidqc/` void/empty-region QC report
     - `cellqc/` cell-level QC report
@@ -170,16 +169,17 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
     - `staining_log.txt` log of the stainings processed by spoQC
     - `report.html` final self-contained HTML report aggregating every spoQC step above
   - `spoQC_tmp/` intermediate data consumed by later spoQC steps
-    - `generalqc_output_hqcr.parquet`, `bubbleqc_output_hqcr.parquet`, `doubletqc_output_hqcr.parquet`, `voidqc_output_hqcr.parquet`, `cellqc_output_hqcr.parquet` per-step HQCR contribution scores
+    - `generalqc_output_hqcr.parquet`, `doubletqc_output_hqcr.parquet`, `voidqc_output_hqcr.parquet`, `cellqc_output_hqcr.parquet` per-step HQCR contribution scores
     - `ambient_output_genes.parquet` ambient RNA gene-signal estimate
-    - `hqcr_output_mask_raw.parquet` / `hqcr_output_mask_smoothed_raw.parquet` combined raw/smoothed HQCR mask
-    - `hqcr_output_mask_smoothed_celltype_refined.parquet` cell-type-refined smoothed HQCR mask
+    - `mask_raw_output_hqcr.parquet` / `mask_smoothed_raw_output_hqcr.parquet` combined raw/smoothed HQCR mask
+    - `traffic_light_output_hqcr.parquet` HQCR traffic-light classification
+    - `mask_smoothed_celltype_refined_output_hqcr.parquet` cell-type-refined smoothed HQCR mask
     - `metrices/hqpr/${staining}/` per-staining HQPR metrics
-    - `hqpr_${staining}_output_mask_raw/` / `hqpr_${staining}_output_mask_smoothed_raw/` per-staining raw/smoothed HQPR mask
+    - `mask_raw_output_hqpr_${staining}/` / `mask_smoothed_raw_output_hqpr_${staining}/` per-staining raw/smoothed HQPR mask
     - `metrices/hqtr/` HQTR metrics
-    - `hqtr_output_ac_prob/` HQTR ambient-contamination probabilities
-    - `hqtr_output_qv_prob/` HQTR quality-value probabilities
-    - `hqtr_output_mask_raw/` / `hqtr_output_mask_smoothed_raw/` raw/smoothed HQTR mask
+    - `ac_density_output_hqtr/` HQTR ambient-contamination probabilities
+    - `qv_density_output_hqtr/` HQTR quality-value probabilities
+    - `mask_raw_output_hqtr/` / `mask_smoothed_raw_output_hqtr/` raw/smoothed HQTR mask
 - `multiqc/`
   - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
   - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.

diff --git a/modules/local/spoQC/ambient/main.nf b/modules/local/spoQC/ambient/main.nf
@@ -6,7 +6,7 @@ process SPOQC_AMBIENT {
     label 'process_mid_time'
     label 'spoqc'
 
-    container "heylf/spoqc_dev:0.1.0"
+    container "heylf/spoqc_dev:0.1.1"
 
     input:
     tuple val(meta), path(spatialdata, stageAs: "*")

diff --git a/modules/local/spoQC/analysis_category/main.nf b/modules/local/spoQC/analysis_category/main.nf
@@ -6,25 +6,23 @@ process SPOQC_ANALYSIS_CATEGORY {
     label 'spoqc'
 
 
-    container "heylf/spoqc_dev:0.1.0"
+    container "heylf/spoqc_dev:0.1.1"
 
     input:
     tuple val(meta), path(spatialdata, stageAs: "*")
     path(annotation, stageAs: "*")
     val(step)
     path(tmp_general, stageAs: "spoQC_tmp/generalqc_output_hqcr.parquet")
-    path(tmp_bubble, stageAs: "spoQC_tmp/bubbleqc_output_hqcr.parquet")
     path(tmp_doublet, stageAs: "spoQC_tmp/doubletqc_output_hqcr.parquet")
     path(tmp_void, stageAs: "spoQC_tmp/voidqc_output_hqcr.parquet")
     path(tmp_cell, stageAs: "spoQC_tmp/cellqc_output_hqcr.parquet")
-    path(mask_hqcr, stageAs: "spoQC_tmp/hqcr_output_mask_raw.parquet")
-    path(mask_smoothed_hqcr, stageAs: "spoQC_tmp/hqcr_output_mask_smoothed_raw.parquet")
-    path(traffic_light_hqcr, stageAs: "spoQC_tmp/traffic_light_output_hqcr.parquet")
-    path(qv, stageAs: "spoQC_tmp/hqtr_output_qv_prob")
-    path(ac, stageAs: "spoQC_tmp/hqtr_output_ac_prob")
+    path(mask_hqcr, stageAs: "spoQC_tmp/mask_raw_output_hqcr.parquet")
+    path(mask_smoothed_hqcr, stageAs: "spoQC_tmp/mask_smoothed_raw_output_hqcr.parquet")
+    path(qv, stageAs: "spoQC_tmp/qv_density_output_hqtr")
+    path(ac, stageAs: "spoQC_tmp/ac_density_output_hqtr")
     path(metrices_hqtr, stageAs: "spoQC_tmp/metrices/hqtr")
-    path(mask_smoothed_hqtr, stageAs: "spoQC_tmp/hqtr_output_mask_smoothed_raw")
-    path(mask_hqtr, stageAs: "spoQC_tmp/hqtr_output_mask_raw")
+    path(mask_smoothed_hqtr, stageAs: "spoQC_tmp/mask_smoothed_raw_output_hqtr")
+    path(mask_hqtr, stageAs: "spoQC_tmp/mask_raw_output_hqtr")
     path(metrices_hqpr, stageAs: "spoQC_tmp/metrices/hqpr/*")
     path(mask_smoothed_hqpr, stageAs: "spoQC_tmp/*")
     path(mask_hqpr, stageAs: "spoQC_tmp/*")

diff --git a/modules/local/spoQC/analysis_category/meta.yml b/modules/local/spoQC/analysis_category/meta.yml
@@ -38,11 +38,6 @@ input:
       description: General QC parquet output from SPOQC_GENERAL
       pattern: "generalqc_output_hqcr.parquet"
       ontologies: []
-  - tmp_bubble:
-      type: file
-      description: Bubble QC parquet output from SPOQC_BUBBLE
-      pattern: "bubbleqc_output_hqcr.parquet"
-      ontologies: []
   - tmp_doublet:
       type: file
       description: Doublet QC parquet output from SPOQC_DOUBLET
@@ -61,12 +56,12 @@ input:
   - mask_hqcr:
       type: file
       description: HQCR raw mask from SPOQC_HQCR_IDENT
-      pattern: "hqcr_output_mask_raw.parquet"
+      pattern: "mask_raw_output_hqcr.parquet"
       ontologies: []
   - mask_smoothed_hqcr:
       type: file
       description: Smoothed HQCR mask from SPOQC_HQCR_IDENT
-      pattern: "hqcr_output_mask_smoothed_raw.parquet"
+      pattern: "mask_smoothed_raw_output_hqcr.parquet"
       ontologies: []
   - traffic_light_hqcr:
       type: file
@@ -76,12 +71,12 @@ input:
   - qv:
       type: directory
       description: HQTR quality-value probability output from SPOQC_HQTR_QV
-      pattern: "hqtr_output_qv_prob"
+      pattern: "qv_density_output_hqtr"
       ontologies: []
   - ac:
       type: directory
       description: HQTR ambient-contamination probability output from SPOQC_HQTR_AC
-      pattern: "hqtr_output_ac_prob"
+      pattern: "ac_density_output_hqtr"
       ontologies: []
   - metrices_hqtr:
       type: directory
@@ -91,12 +86,12 @@ input:
   - mask_smoothed_hqtr:
       type: directory
       description: Smoothed HQTR mask from SPOQC_HQTR_REFINEMENT
-      pattern: "hqtr_output_mask_smoothed_raw"
+      pattern: "mask_smoothed_raw_output_hqtr"
       ontologies: []
   - mask_hqtr:
       type: directory
       description: HQTR raw mask from SPOQC_HQTR_CLUSTERING
-      pattern: "hqtr_output_mask_raw"
+      pattern: "mask_raw_output_hqtr"
       ontologies: []
   - metrices_hqpr:
       type: directory

diff --git a/modules/local/spoQC/analysis_category/tests/main.nf.test b/modules/local/spoQC/analysis_category/tests/main.nf.test
@@ -56,16 +56,6 @@ nextflow_process {
             }
         }
 
-        run("SPOQC_BUBBLE") {
-            script "modules/local/spoQC/bubble/main.nf"
-            process {
-                """
-                input[0] = SPATIALDATA_WRITE.out.spatialdata
-                input[1] = "bubbleqc"
-                """
-            }
-        }
-
         run("SPOQC_DOUBLET") {
             script "modules/local/spoQC/doublet/main.nf"
             process {
@@ -104,10 +94,9 @@ nextflow_process {
                 input[0] = SPATIALDATA_WRITE.out.spatialdata
                 input[1] = "hqcr_ident"
                 input[2] = SPOQC_GENERAL.out.tmp.map { it[1] }
-                input[3] = SPOQC_BUBBLE.out.tmp.map { it[1] }
-                input[4] = SPOQC_DOUBLET.out.tmp.map { it[1] }
-                input[5] = SPOQC_VOID.out.tmp.map { it[1] }
-                input[6] = SPOQC_CELL.out.tmp.map { it[1] }
+                input[3] = SPOQC_DOUBLET.out.tmp.map { it[1] }
+                input[4] = SPOQC_VOID.out.tmp.map { it[1] }
+                input[5] = SPOQC_CELL.out.tmp.map { it[1] }
                 """
             }
         }
@@ -219,21 +208,19 @@ nextflow_process {
                 input[1] = SPOQC_ANNOTATION.out.annotation.map { it[1] }
                 input[2] = "analysis_category"
                 input[3] = SPOQC_GENERAL.out.tmp.map { it[1] }
-                input[4] = SPOQC_BUBBLE.out.tmp.map { it[1] }
-                input[5] = SPOQC_DOUBLET.out.tmp.map { it[1] }
-                input[6] = SPOQC_VOID.out.tmp.map { it[1] }
-                input[7] = SPOQC_CELL.out.tmp.map { it[1] }
-                input[8] = SPOQC_HQCR_IDENT.out.mask.map { it[1] }
-                input[9] = SPOQC_HQCR_IDENT.out.mask_smoothed.map { it[1] }
-                input[10] = SPOQC_HQCR_IDENT.out.traffic_light.map { it[1] }
-                input[11] = SPOQC_HQTR_QV.out.tmp.map { it[1] }
-                input[12] = SPOQC_HQTR_AC.out.tmp.map { it[1] }
-                input[13] = SPOQC_HQTR_METRICES.out.metrices.map { it[1] }
-                input[14] = SPOQC_HQTR_REFINEMENT.out.mask_smoothed.map { it[1] }
-                input[15] = SPOQC_HQTR_CLUSTERING.out.mask.map { it[1] }
-                input[16] = SPOQC_HQPR_METRICES.out.metrices.map { _meta, _staining, p -> p }.collect()
-                input[17] = SPOQC_HQPR_REFINEMENT.out.mask_smoothed.map { _meta, _staining, p -> p }.collect()
-                input[18] = SPOQC_HQPR_CLUSTERING.out.mask.map { _meta, _staining, p -> p }.collect()
+                input[4] = SPOQC_DOUBLET.out.tmp.map { it[1] }
+                input[5] = SPOQC_VOID.out.tmp.map { it[1] }
+                input[6] = SPOQC_CELL.out.tmp.map { it[1] }
+                input[7] = SPOQC_HQCR_IDENT.out.mask.map { it[1] }
+                input[8] = SPOQC_HQCR_IDENT.out.mask_smoothed.map { it[1] }
+                input[9] = SPOQC_HQTR_QV.out.tmp.map { it[1] }
+                input[10] = SPOQC_HQTR_AC.out.tmp.map { it[1] }
+                input[11] = SPOQC_HQTR_METRICES.out.metrices.map { it[1] }
+                input[12] = SPOQC_HQTR_REFINEMENT.out.mask_smoothed.map { it[1] }
+                input[13] = SPOQC_HQTR_CLUSTERING.out.mask.map { it[1] }
+                input[14] = SPOQC_HQPR_METRICES.out.metrices.map { _meta, _staining, p -> p }.collect()
+                input[15] = SPOQC_HQPR_REFINEMENT.out.mask_smoothed.map { _meta, _staining, p -> p }.collect()
+                input[16] = SPOQC_HQPR_CLUSTERING.out.mask.map { _meta, _staining, p -> p }.collect()
                 """
             }
         }
@@ -258,21 +245,19 @@ nextflow_process {
                 input[1] = SPOQC_ANNOTATION.out.annotation.map { it[1] }
                 input[2] = "analysis_category"
                 input[3] = SPOQC_GENERAL.out.tmp.map { it[1] }
-                input[4] = SPOQC_BUBBLE.out.tmp.map { it[1] }
-                input[5] = SPOQC_DOUBLET.out.tmp.map { it[1] }
-                input[6] = SPOQC_VOID.out.tmp.map { it[1] }
-                input[7] = SPOQC_CELL.out.tmp.map { it[1] }
-                input[8] = SPOQC_HQCR_IDENT.out.mask.map { it[1] }
-                input[9] = SPOQC_HQCR_IDENT.out.mask_smoothed.map { it[1] }
-                input[10] = SPOQC_HQCR_IDENT.out.traffic_light.map { it[1] }
-                input[11] = SPOQC_HQTR_QV.out.tmp.map { it[1] }
-                input[12] = SPOQC_HQTR_AC.out.tmp.map { it[1] }
-                input[13] = SPOQC_HQTR_METRICES.out.metrices.map { it[1] }
-                input[14] = SPOQC_HQTR_REFINEMENT.out.mask_smoothed.map { it[1] }
-                input[15] = SPOQC_HQTR_CLUSTERING.out.mask.map { it[1] }
-                input[16] = SPOQC_HQPR_METRICES.out.metrices.map { _meta, _staining, p -> p }.collect()
-                input[17] = SPOQC_HQPR_REFINEMENT.out.mask_smoothed.map { _meta, _staining, p -> p }.collect()
-                input[18] = SPOQC_HQPR_CLUSTERING.out.mask.map { _meta, _staining, p -> p }.collect()
+                input[4] = SPOQC_DOUBLET.out.tmp.map { it[1] }
+                input[5] = SPOQC_VOID.out.tmp.map { it[1] }
+                input[6] = SPOQC_CELL.out.tmp.map { it[1] }
+                input[7] = SPOQC_HQCR_IDENT.out.mask.map { it[1] }
+                input[8] = SPOQC_HQCR_IDENT.out.mask_smoothed.map { it[1] }
+                input[9] = SPOQC_HQTR_QV.out.tmp.map { it[1] }
+                input[10] = SPOQC_HQTR_AC.out.tmp.map { it[1] }
+                input[11] = SPOQC_HQTR_METRICES.out.metrices.map { it[1] }
+                input[12] = SPOQC_HQTR_REFINEMENT.out.mask_smoothed.map { it[1] }
+                input[13] = SPOQC_HQTR_CLUSTERING.out.mask.map { it[1] }
+                input[14] = SPOQC_HQPR_METRICES.out.metrices.map { _meta, _staining, p -> p }.collect()
+                input[15] = SPOQC_HQPR_REFINEMENT.out.mask_smoothed.map { _meta, _staining, p -> p }.collect()
+                input[16] = SPOQC_HQPR_CLUSTERING.out.mask.map { _meta, _staining, p -> p }.collect()
                 """
             }
         }

diff --git a/modules/local/spoQC/analysis_cluster/main.nf b/modules/local/spoQC/analysis_cluster/main.nf
@@ -6,25 +6,24 @@ process SPOQC_ANALYSIS_CLUSTER {
     label 'spoqc'
 
 
-    container "heylf/spoqc_dev:0.1.0"
+    container "heylf/spoqc_dev:0.1.1"
 
     input:
     tuple val(meta), path(spatialdata, stageAs: "*")
     path(annotation, stageAs: "*")
     val(step)
     path(tmp_general, stageAs: "spoQC_tmp/generalqc_output_hqcr.parquet")
-    path(tmp_bubble, stageAs: "spoQC_tmp/bubbleqc_output_hqcr.parquet")
     path(tmp_doublet, stageAs: "spoQC_tmp/doubletqc_output_hqcr.parquet")
     path(tmp_void, stageAs: "spoQC_tmp/voidqc_output_hqcr.parquet")
     path(tmp_cell, stageAs: "spoQC_tmp/cellqc_output_hqcr.parquet")
-    path(mask_hqcr, stageAs: "spoQC_tmp/hqcr_output_mask_raw.parquet")
-    path(mask_smoothed_hqcr, stageAs: "spoQC_tmp/hqcr_output_mask_smoothed_raw.parquet")
+    path(mask_hqcr, stageAs: "spoQC_tmp/mask_raw_output_hqcr.parquet")
+    path(mask_smoothed_hqcr, stageAs: "spoQC_tmp/mask_smoothed_raw_output_hqcr.parquet")
     path(traffic_light_hqcr, stageAs: "spoQC_tmp/traffic_light_output_hqcr.parquet")
-    path(qv, stageAs: "spoQC_tmp/hqtr_output_qv_prob")
-    path(ac, stageAs: "spoQC_tmp/hqtr_output_ac_prob")
+    path(qv, stageAs: "spoQC_tmp/qv_density_output_hqtr")
+    path(ac, stageAs: "spoQC_tmp/ac_density_output_hqtr")
     path(metrices_hqtr, stageAs: "spoQC_tmp/metrices/hqtr")
-    path(mask_smoothed_hqtr, stageAs: "spoQC_tmp/hqtr_output_mask_smoothed_raw")
-    path(mask_hqtr, stageAs: "spoQC_tmp/hqtr_output_mask_raw")
+    path(mask_smoothed_hqtr, stageAs: "spoQC_tmp/mask_smoothed_raw_output_hqtr")
+    path(mask_hqtr, stageAs: "spoQC_tmp/mask_raw_output_hqtr")
     path(metrices_hqpr, stageAs: "spoQC_tmp/metrices/hqpr/*")
     path(mask_smoothed_hqpr, stageAs: "spoQC_tmp/*")
     path(mask_hqpr, stageAs: "spoQC_tmp/*")

diff --git a/modules/local/spoQC/analysis_cluster/meta.yml b/modules/local/spoQC/analysis_cluster/meta.yml
@@ -40,11 +40,6 @@ input:
       description: General QC parquet output from SPOQC_GENERAL
       pattern: "generalqc_output_hqcr.parquet"
       ontologies: []
-  - tmp_bubble:
-      type: file
-      description: Bubble QC parquet output from SPOQC_BUBBLE
-      pattern: "bubbleqc_output_hqcr.parquet"
-      ontologies: []
   - tmp_doublet:
       type: file
       description: Doublet QC parquet output from SPOQC_DOUBLET
@@ -63,12 +58,17 @@ input:
   - mask_hqcr:
       type: file
       description: HQCR raw mask from SPOQC_HQCR_IDENT
-      pattern: "hqcr_output_mask_raw.parquet"
+      pattern: "mask_raw_output_hqcr.parquet"
       ontologies: []
   - mask_smoothed_hqcr:
       type: file
       description: Smoothed HQCR mask from SPOQC_HQCR_IDENT
-      pattern: "hqcr_output_mask_smoothed_raw.parquet"
+      pattern: "mask_smoothed_raw_output_hqcr.parquet"
+      ontologies: []
+  - traffic_light_hqcr:
+      type: file
+      description: HQCR traffic-light classification from SPOQC_HQCR_IDENT
+      pattern: "traffic_light_output_hqcr.parquet"
       ontologies: []
   - traffic_light_hqcr:
       type: file
@@ -78,12 +78,12 @@ input:
   - qv:
       type: directory
       description: HQTR quality-value probability output from SPOQC_HQTR_QV
-      pattern: "hqtr_output_qv_prob"
+      pattern: "qv_density_output_hqtr"
       ontologies: []
   - ac:
       type: directory
       description: HQTR ambient-contamination probability output from SPOQC_HQTR_AC
-      pattern: "hqtr_output_ac_prob"
+      pattern: "ac_density_output_hqtr"
       ontologies: []
   - metrices_hqtr:
       type: directory
@@ -93,12 +93,12 @@ input:
   - mask_smoothed_hqtr:
       type: directory
       description: Smoothed HQTR mask from SPOQC_HQTR_REFINEMENT
-      pattern: "hqtr_output_mask_smoothed_raw"
+      pattern: "mask_smoothed_raw_output_hqtr"
       ontologies: []
   - mask_hqtr:
       type: directory
       description: HQTR raw mask from SPOQC_HQTR_CLUSTERING
-      pattern: "hqtr_output_mask_raw"
+      pattern: "mask_raw_output_hqtr"
       ontologies: []
   - metrices_hqpr:
       type: directory