nf-core · heylf · Jul 23, 2026 · Jul 23, 2026 · Jul 27, 2026 · Jul 27, 2026
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
@@ -81,7 +81,7 @@ jobs:
           - isMain: true
             profile: "conda"
         NXF_VER:
-          - "25.04.0"
+          - "26.04.6"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,12 +9,31 @@ 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).
+- 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`
+- New samplesheet for a full test: `assets/samplesheet_full.csv` with `conf/test_full.config`.
+- `conf/base.config`: adding combinatorial label system — separate `process_{tiny,low,mid,high,xl}_cpus`, `_mem`, and `_time` labels, each scaling with `task.attempt`.
+- Added `nf-core/unzip` module usage so the pipeline can unpack the larger test dataset.
+- samplesheet redefinition: `sample,bundle,image,annotation,stainings`, samplesheet allows for two additional optional columns `annotation,stainings` that are useful for the QC subworkflow.
+- `spatialdata_write_meta_merge/main.nf`: Change to subworkflow to account for proper `qc` mode.
+- Change to `bin/spatialdata_write.py`: Adding an `all` mode to set all available features to `True`, which is important for QC.
+
 ### `Fixed`
 
+- Change to input validation in `spatialaxe.nf`: Moving `morphology_focus/` folder into `bundle_optional_files` because not all Xenium bundles have such a folder.
+
 ### `Dependencies`
 
 ### `Deprecated`
 
+- `nextflow.config`: bumped the `nf-schema` plugin version.
+- `subworkflows/nf-core/utils_nfschema_plugin/main.nf`: added a new `cli_typecast` input (pass `null` to keep default behavior), renamed the `parametersSchema` option key to `parameters_schema` across the help/summary/validate option maps, and fixed how the `--help` text value is resolved.
+- `subworkflows/nf-core/utils_nextflow_pipeline/main.nf`: bumped the version.
+- `subworkflows/local/utils_nfcore_spatialaxe_pipeline/main.nf`: passes the new `cli_typecast` argument (`null`) through to `UTILS_NFSCHEMA_PLUGIN`.
+- `nextflow_schema.json`: cleanup driven by the new schema version.
+
 ## 1.0.1 - [06.08.2026]
 
 Hotfix to tackle some bugs

diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@
 [![GitHub Actions Linting Status](https://github.com/nf-core/spatialaxe/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/spatialaxe/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/spatialaxe/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.20733817-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.20733817)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A526.04.6-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
 [![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
@@ -48,6 +48,7 @@ The pipeline supports the following tools:
 - QC methods:
   - [MultiQC Xenium Extra Plugin](https://github.com/MultiQC/xenium-extra)
   - [OPT](https://github.com/JEFworks-Lab/off-target-probe-tracker)
+  - [spoQC](https://github.com/heylf/spoQC)
 
 ## Usage
 

diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
@@ -1,2 +1,2 @@
-sample,bundle,image
-test_run,https://raw.githubusercontent.com/nf-core/test-datasets/spatialaxe/xenium_bundle.tar.gz,
+sample,bundle,image,annotation,stainings
+test_run,https://raw.githubusercontent.com/nf-core/test-datasets/spatialaxe/xenium_bundle.tar.gz,,,0;
diff --git a/assets/samplesheet_full.csv b/assets/samplesheet_full.csv
@@ -0,0 +1,2 @@
+sample,bundle,image,annotation,stainings
+test_run_full,https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/Xenium_V1_Protein_Human_Kidney_tiny_outs.zip,,,0;1
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -22,6 +22,16 @@
                 "type": "string",
                 "pattern": "^\\S+$",
                 "errorMessage": "You can provide an image. If you do not then please leave the field empty."
+            },
+            "annotation": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "You can provide an annotation. If you do not then please leave the field empty."
+            },
+            "stainings": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "The indices of the image channels of the individual stainings you want to analyse."
             }
         },
         "required": ["sample", "bundle"]

diff --git a/bin/spatialdata_write.py b/bin/spatialdata_write.py
@@ -130,6 +130,17 @@ def main():
         nucleus_labels = False
         cells_as_circles = False
 
+    # set sd variables based on the coordinate space
+    if args.coordinate_space == "all":
+        cells_labels = True
+        nucleus_labels = True
+        cells_boundaries = True
+        nucleus_boundaries = True
+        cells_as_circles = True
+
+    print(f"[NOTE] Apply cells_boundaries {cells_boundaries}")
+    print(f"[NOTE] Apply nucleus_boundaries {nucleus_boundaries}")
+
     if args.format == "xenium":
         sd_xenium_obj = xenium(
             args.bundle,

diff --git a/conf/base.config b/conf/base.config
@@ -80,6 +80,82 @@ process {
         maxRetries    = 2
     }
 
+    // =========================================================================
+    // Combinatorial CPU labels
+    // =========================================================================
+
+    // =========================
+    // CPU
+    // =========================
+
+    withLabel:process_tiny_cpu {
+        cpus   = { 1 * task.attempt }
+    }
+
+    withLabel:process_low_cpus {
+        cpus   = { 4 * task.attempt }
+    }
+
+    withLabel:process_mid_cpus {
+        cpus   = { 8 * task.attempt }
+    }
+
+    withLabel:process_high_cpus {
+        cpus   = { 12 * task.attempt }
+    }
+
+    withLabel:process_xl_cpus {
+        cpus   = { 30 * task.attempt }
+    }
+
+    // =========================
+    // Memory
+    // =========================
+
+    withLabel:process_tiny_mem {
+        memory = { 10.GB * task.attempt }
+    }
+
+    withLabel:process_low_mem {
+        memory = { 30.GB * task.attempt }
+    }
+
+    withLabel:process_mid_mem {
+        memory = { 50.GB * task.attempt }
+    }
+
+    withLabel:process_high_mem {
+        memory = { 100.GB * task.attempt }
+    }
+
+    withLabel:process_xl_mem {
+        memory = { 250.GB * task.attempt }
+    }
+
+    // =========================
+    // Time
+    // =========================
+
+    withLabel:process_tiny_time {
+        time   = { 4.h * task.attempt }
+    }
+
+    withLabel:process_low_time {
+        time   = { 8.h * task.attempt }
+    }
+
+    withLabel:process_mid_time {
+        time   = { 16.h * task.attempt }
+    }
+
+    withLabel:process_high_time {
+        time   = { 24.h * task.attempt }
+    }
+
+    withLabel:process_xl_time {
+        time   = { 72.h * task.attempt }
+    }
+
     // =========================================================================
     // GPU labels
     // =========================================================================
@@ -100,4 +176,18 @@ process {
         time   = { 16.h * task.attempt }
     }
 
+    // =========================================================================
+    // Extra labels
+    // =========================================================================
+
+    // That needs to be included for some processes, esle kalleido failes because of tmp dir issues.
+    withLabel:spoqc {
+        beforeScript = {
+            """
+            export TMPDIR=\${SLURM_TMPDIR:-\$NXF_TASK_WORKDIR/tmp}
+            mkdir -p \$TMPDIR
+            """
+        }
+    }
+
 }
diff --git a/conf/modules.config b/conf/modules.config
@@ -378,4 +378,13 @@ process {
             mode: params.publish_dir_mode,
         ]
     }
+
+    // ---------------------------- spoQC -----------------------------------------
+
+    withName: '.*SPOQC_.*' {
+        publishDir = [
+            path: { "${params.outdir}/spoqc/${meta.id}" },
+            mode: params.publish_dir_mode,
+        ]
+    }
 }
diff --git a/conf/test_full.config b/conf/test_full.config
@@ -15,6 +15,7 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data
-    input  = "${projectDir}/assets/samplesheet.csv"
+    input  = "${projectDir}/assets/samplesheet_full.csv"
+    outdir = 'results'
     mode   = 'coordinate'
 }
diff --git a/conf/tests/test_full_spoqc.config b/conf/tests/test_full_spoqc.config
@@ -0,0 +1,35 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/spatialaxe -profile test,<docker/singularity> --mode <MODE> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+process {
+
+    resourceLimits = [
+        cpus: 4,
+        memory: '14.GB',
+        time: '2.h'
+    ]
+
+    withName: UNTAR {
+        ext.prefix = "test_bundle"
+    }
+}
+
+params {
+    config_profile_name        = 'Test profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+
+    // Input data
+    input                      = "${projectDir}/assets/samplesheet_full.csv"
+    outdir                     = 'results'
+    mode                       = 'qc'
+    spoqc                      = true
+}
diff --git a/conf/tests/test_spoqc.config b/conf/tests/test_spoqc.config
@@ -0,0 +1,35 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/spatialaxe -profile test,<docker/singularity> --mode <MODE> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+process {
+
+    resourceLimits = [
+        cpus: 4,
+        memory: '14.GB',
+        time: '2.h'
+    ]
+
+    withName: UNTAR {
+        ext.prefix = "test_bundle"
+    }
+}
+
+params {
+    config_profile_name        = 'Test profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+
+    // Input data
+    input                      = "${projectDir}/assets/samplesheet.csv"
+    outdir                     = 'results'
+    mode                       = 'qc'
+    spoqc                      = true
+}
diff --git a/docs/output.md b/docs/output.md
@@ -22,6 +22,10 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
   - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
   - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
+## Quality Control
+
+[Quality Control](qc.md): An overview of the different QC reports.
+
 ## Image mode
 
 <details markdown="1">
@@ -127,6 +131,55 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
     - `*.tsv` TSV file containing the gene and transcript information to which each probe aligns
   - `stat/`
     - `*.tsv` TSV file containing the summary stats
+- `spoqc/`
+  - `report/`
+    - `annotation/`
+      - `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
+    - `ambientqc/` ambient-RNA (background gene) QC report
+    - `hqcr/`
+      - `hqcr_ident/` high-quality cell region (HQCR) identification report
+      - `hqcr_celltype/` cell-type-refined HQCR report
+    - `hqpr/`
+      - `hqpr_metrices/${staining}/` per-staining high-quality pixel region (HQPR) metrics report
+      - `hqpr_clustering/${staining}/` per-staining HQPR clustering report
+      - `hqpr_refinement/${staining}/` per-staining HQPR mask refinement report
+      - `hqpr_bounding_box/${staining}/` per-staining HQPR bounding-box report
+    - `hqtr/`
+      - `hqtr_metrices/` high-quality transcript region (HQTR) metrics report
+      - `hqtr_ac/` HQTR ambient-contamination probability report
+      - `hqtr_qv/` HQTR quality-value probability report
+      - `hqtr_clustering/` HQTR clustering report
+      - `hqtr_refinement/` HQTR mask refinement report
+      - `hqtr_bounding_box/` HQTR bounding-box report
+    - `combine_masks/${staining}/` report combining the HQCR, HQPR and HQTR masks per staining
+    - `transcriptqc/` transcript-level QC report (against the reference gene panel)
+    - `cellcycleqc/` cell-cycle scoring QC report
+    - `modelqc/` model-based QC scoring report
+    - `analysis/`
+      - `overview/` downstream QC analysis overview report
+      - `rna_qc_annotated.h5ad` AnnData object annotated with the combined QC results
+      - `category/` downstream per-category QC analysis report
+      - `cluster/` downstream clustering QC analysis report
+      - `rna_cluster.h5ad` AnnData object with clustering results
+    - `staining_log.txt` log of the stainings processed by spoQC
+    - `report.html` final self-contained HTML report aggregating every spoQC step above
+  - `spoQC_tmp/` intermediate data consumed by later spoQC steps
+    - `generalqc_output_hqcr.parquet`, `bubbleqc_output_hqcr.parquet`, `doubletqc_output_hqcr.parquet`, `voidqc_output_hqcr.parquet`, `cellqc_output_hqcr.parquet` per-step HQCR contribution scores
+    - `ambient_output_genes.parquet` ambient RNA gene-signal estimate
+    - `hqcr_output_mask_raw.parquet` / `hqcr_output_mask_smoothed_raw.parquet` combined raw/smoothed HQCR mask
+    - `hqcr_output_mask_smoothed_celltype_refined.parquet` cell-type-refined smoothed HQCR mask
+    - `metrices/hqpr/${staining}/` per-staining HQPR metrics
+    - `hqpr_${staining}_output_mask_raw/` / `hqpr_${staining}_output_mask_smoothed_raw/` 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
 - `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.
@@ -164,7 +217,7 @@ The pipeline create spatialdata objects (data bundles) on various stages (see me
 
 </details>
 
-### Xenium Ranger Import Segmentation)
+### Xenium Ranger Import Segmentation
 
 This step is needed to import segemntations from different methods into the xenium bundle and is called at different stages of the pipeline.
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		sample,bundle,image,annotation,stainings
		test_run_full,https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/Xenium_V1_Protein_Human_Kidney_tiny_outs.zip,,,0;1