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,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" },
+            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: 8,
+        memory: '30.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                      = "${projectDir}/assets/samplesheet_full.csv"
+    outdir                     = 'results'
+    mode                       = 'qc'
+    spoqc                      = true
+}
diff --git a/conf/tests/test_spoqc.config b/conf/tests/test_spoqc.config
@@ -0,0 +1,35 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/spatialaxe -profile test,<docker/singularity> --mode <MODE> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+process {
+
+    resourceLimits = [
+        cpus: 8,
+        memory: '30.GB',
+        time: '2.h'
+    ]
+
+    withName: UNTAR {
+        ext.prefix = "test_bundle"
+    }
+}
+
+params {
+    config_profile_name        = 'Test profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+
+    // Input data
+    input                      = "${projectDir}/assets/samplesheet.csv"
+    outdir                     = 'results'
+    mode                       = 'qc'
+    spoqc                      = true
+}
diff --git a/docs/output.md b/docs/output.md
@@ -21,6 +21,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
   - [Xenium Ranger import segmentation](#xenium-ranger-import-segmentation)
   - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
   - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
+  - [spoQC](https://github.com/heylf/spoQC) - Report and QC metrics (see [documentation of spoQC](soon))
 
 ## Image mode
 
@@ -127,6 +128,55 @@ 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.

diff --git a/docs/usage.md b/docs/usage.md
@@ -106,9 +106,21 @@ nextflow run nf-core/spatialaxe \
    --mode qc
 ```
 
+To run [spoQC](https://github.com/heylf/spoQC) you have to set an additional option:
+
+```bash
+nextflow run nf-core/spatialaxe \
+   -profile <docker/singularity/.../institute> \
+   --input samplesheet.csv \
+   --outdir <OUTDIR> \
+   --mode qc \
+   --spoqc true
+```
+
 - 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)
 
 ### Image-based Segmentation mode (--mode image): <br>
 

diff --git a/main.nf b/main.nf
@@ -79,6 +79,7 @@ workflow NFCORE_SPATIALAXE {
         params.stardist_nuclei_model,
         params.tiling,
         params.xeniumranger_only,
+        params.spoqc,
     )
     emit:
     multiqc_report = SPATIALAXE.out.multiqc_report // channel: /path/to/multiqc_report.html
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		sample,bundle,image,annotation,stainings
		test_run,https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/Xenium_V1_Protein_Human_Kidney_tiny_outs.zip,,,0;1