cbib/SpaceBlocks

None

Overview

Latest release: v0.3.0, Last update: 2026-09-03

Share link: https://snakemake.github.io/snakemake-workflow-catalog?wf=cbib/SpaceBlocks

Quality control: linting: failed formatting: passed

Workflow Rule Graph

This visualization of the workflow’s rule graph was automatically generated using Snakevision

Deployment

Step 1: Install Snakemake and Snakedeploy

Snakemake and Snakedeploy are best installed via the Conda package manager. It is recommended to install conda via Miniforge. Run

conda create -c conda-forge -c bioconda -c nodefaults --name snakemake snakemake snakedeploy

to install both Snakemake and Snakedeploy in an isolated environment. For all following commands ensure that this environment is activated via

conda activate snakemake

For other installation methods, refer to the Snakemake and Snakedeploy documentation.

Step 2: Deploy workflow

With Snakemake and Snakedeploy installed, the workflow can be deployed as follows. First, create an appropriate project working directory on your system and enter it:

mkdir -p path/to/project-workdir
cd path/to/project-workdir

In all following steps, we will assume that you are inside of that directory. Then run

snakedeploy deploy-workflow https://github.com/cbib/SpaceBlocks . --tag v0.3.0

Snakedeploy will create two folders, workflow and config. The former contains the deployment of the chosen workflow as a Snakemake module, the latter contains configuration files which will be modified in the next step in order to configure the workflow to your needs.

Step 4: Run workflow

The deployment method is controlled using the --software-deployment-method (short --sdm) argument.

To run the workflow with automatic deployment of all required software via conda/mamba, use

snakemake --cores all --sdm conda

Snakemake will automatically detect the main Snakefile in the workflow subfolder and execute the workflow module that has been defined by the deployment in step 2.

For further options such as cluster and cloud execution, see the docs.

Step 5: Generate report

After finalizing your data analysis, you can automatically generate an interactive visual HTML report for inspection of results together with parameters and code inside of the browser using

snakemake --report report.zip

Configuration

The following section is imported from the workflow’s config/README.md.

This page explains how to fully set up the config files to run SpaceBlocks. Full documentation can be found at https://cbib.github.io/SpaceBlocks/configuration/.

SpaceBlocks is configured through config/config.yaml, which contains all the parameters needed for the run, plus one or two sample sheets.

The explanations on this page are divided by type (directory, parameter, color, and so on). In the config file, parameters are divided by Block and function.

Every key in config/config.yaml is validated against workflow/schemas/config.schema.yaml before the run starts, so a typo or a missing required field fails immediately with a clear message.

!!! note “Snakemake-catalog page” The full, always-updated table of every parameter (type, default, required) is generated automatically from the schema and shown on the workflow’s Snakemake-catalog page. This page covers the how and the why; the schema is the exhaustive reference.

1. Choose a mode

mode selects which Headblock builds the standardized contract h5ad (or none):

!!! warning “Space Ranger installation” The Visium HD HeadBlock additionally needs an external Space Ranger installation.

`config["mode"]`	Head that runs	Input
`visiumhd`	`spaceranger_count_vhd` → `generate_qupath_vhd` → `prepare_input_vhd`	10x Visium HD fastqs + Space Ranger
`xenium5k`	`convert_zarr_x5k` → `generate_qupath_x5k` → `prepare_input_x5k`	Xenium output bundle
`atera`	`convert_zarr_ate` → `generate_qupath_ate` → `prepare_input_ate`	Atera output bundle; optional registered H&E inputs
`merscope`	`generate_qupath_mer` → `prepare_input_mer`	MERSCOPE region directory
`decoupled`	(none)	Pre-existing contract h5ad files you provide

The analysis CoreBlocks are identical in all five cases. Atera support is currently alpha because the public preview format may change before commercial release.

2. Paths, files and sample sheets

The SpaceBlocks config/config.yaml sets the input and output directories, and gets the sample information and metadata (for integration and plotting) from one or two TSV files, depending on the config["mode"] set.

Path / File	Key	Condition	Meaning
Path	`spaceranger_processing_outdir`	Head modes	Directory where the head writes heavy intermediates such as Space Ranger outputs or SpatialData Zarr stores.
File	`spaceranger`	`mode: visiumhd`	Path to the Space Ranger installation.
File	`probe_set`	`mode: visiumhd`	Probe set CSV needed to run Space Ranger.
File	`transcriptome`	`mode: visiumhd`	Reference transcriptome needed to run Space Ranger.
Path	`post_processing_outdir`	Mandatory	Output directory root; it will contain the result folders for the run.
Path	`logdir`	Mandatory	Directory for per-rule logs and benchmarks.
Path	`geojson_path`	Optional, recommended	Directory containing the GeoJSONs that annotate spatial regions for each sample (see the QuPath tutorial).
Path	`contract_dir`	`mode: decoupled`	Directory holding the pre-existing contract h5ads to analyse.
File	`per_sample_qc`	Optional (per-sample filters)	TSV of sample-specific QC filters. If empty, the same `analysis.` thresholds apply to every sample (default*).
File	`snakemake_cell_markers`	Optional (pre-annotation)	TSV of canonical marker genes drawn on the Leiden diagnostic plots (`leiden_analysis`) to guide manual annotation.
File	`gene_exploration.queries` (`config/gene_queries.tsv`)	Exploration Coreblock	Genes / gene sets to score (AUCell) and plot in the exploration block.
File	`ingest_ref`	Optional (auto-annotation)	Annotated scRNA-seq reference h5ad for `ingest_ref`.
Path	`precomputed_metadata_dir`	Optional (reproducibility)	Directory of precomputed per-sample metadata TSVs. The metadata can contain precomputed clusters and/or external annotations.

core_samples.tsv is the technology-agnostic sample sheet used by the CoreBlocks in every use case. Visium HD additionally uses visiumhd_samples.csv for fastq, slide, and capture-area information.

For xenium5k, atera, and merscope, per-sample input bundles are located through the corresponding {sample} path pattern in xenium5k.xenium_dir, atera.atera_dir, or merscope.merscope_dir; no second head-specific sample sheet is required.

!!! tip “Color customization for result visualization” You can customize the color scale for any sample metadata in core_samples.tsv as additional columns. See section 3 and section 4 for details.

Sample sheet	Condition	Role
`config/core_samples.tsv`	Mandatory	The technology-agnostic anchor: one row per sample. The first column is the sample name; any further columns are design metadata (e.g. `patient`, `condition`, `type`) that are stamped into `obs` and can be surfaced downstream.
`config/visiumhd_samples.csv`	`mode: visiumhd`	The Visium HD head sheet: fastq directories (plus any re-sequencing runs), slide, and area per sample.

3. Parameters

Parameters are settings that live exclusively in config/config.yaml and determine the details of the run.

Parameter	Condition	Role
`mode`	Mandatory	Which headblock builds the contract (see section 1).
`random_seed`	Reproducibility	Seed for stochastic steps (subsampling, sketching). Note that UMAP/Leiden are not fully deterministic across systems (see section 6).
`use_precomputed_clusters`	Optional (reproducibility)	If `true`, reuse Leiden clusters/metadata from `precomputed_metadata_dir` instead of recomputing them.
`ingest_ref_label_key`	`ingest_ref` reference set	Column in the `ingest_ref` reference that holds the reference cell-type labels.
`integration.integrate_key`	Mandatory	Variable Harmony corrects over during integration (e.g. `sample`).
`extra_annotations.columns`	Optional	`core_samples.tsv` columns to carry into `obs` and surface in downstream plots (e.g. `[patient, batch]`).

4. Color scale customization

In SpaceBlocks, color scales are fully customizable and consistent across analysis plots.

!!! warning “Undefined variable levels are colored in grey” When customizing color palettes, levels not explicitly listed fall back to grey, so a value that renders grey usually means a missing key. If you wish to customize visualization, list all levels in a variable and assign a color for each of them.

To set a given color scale, you just need to specify the HEX color code for each level in config/config.yaml. There are three palette families, each keyed by column → level → hex:

# Sample-metadata palettes — one block per column listed in extra_annotations.columns
sample_colors:
  patient:
    "Patient 1": "#000000"
    "Patient 2": "#E69F00"
  batch:
    "Batch 1": "#8E44AD"

# Cell-type palettes — one block per annotation column (tsv / external / …)
annotation_colors:
  cell_type_tsv:
    "Tcells": "#1f77b4"
    "Fibroblasts": "#2ca02c"
  cell_type_external:          # declare explicitly; not inherited from cell_type_tsv
    "Tcells": "#1f77b4"

# Region palette — lives under analysis, keyed by the region_levels
analysis:
  region_colors:
    "Tumor area": "#46337EFF"
    "Healthy area": "#FDE725FF"

Spatial niches are coloured automatically from a deterministic palette unless you add a spatial_niche block under annotation_colors.

5. Key sections

The rest of the configuration lives in nested blocks. Files and single parameters are covered in section 2 and section 3; colour palettes in section 4.

Section	Condition	What it configures
`xenium5k`	`mode: xenium5k`	Xenium head settings: `xenium_dir`, `zarr_dir`, pyramid levels, and `pixel_size_um`.
`atera`	`mode: atera`	Atera head settings: `atera_dir`, Zarr and pyramid options, plus optional registered H&E image, alignment, and keypoint patterns.
`merscope`	`mode: merscope`	MERSCOPE head settings: `merscope_dir`, selected z-plane, embedded-image resolution, and image channels.
`contract`	Mandatory	Semantic keys of the hand-off object: `sample_key`, `spatial_key`, `require_region`, `require_raw_counts`, `mito_prefix`.
`analysis`	Mandatory	The bulk of the run: QC filters (`min_counts` / `min_genes` / `min_cells` / `max_counts` / `max_pct_mt`), the Leiden `resolution_scan_`, the pseudobulk `analysis_levels` + thresholds, the `region_levels`, and the `run_` toggles. Per-sample QC overrides come from `per_sample_qc`.
`resources`	Mandatory	Per-rule `mem_mb` / `runtime` / `threads` (with a `default`). Memory scales with the retry attempt, so an OOM-killed job is resubmitted with more RAM.
`external_annotation`	optional	Overlay labels from an external tool: `enabled`, `column`, `keep_unannotated` (see section 6).
`qc_sweep`	optional	Candidate-threshold QC diagnostics (never filters).
`spatial_niches`	optional	BANKSY niche detection across concatenated samples.
`subcompartments`	optional	Named cell-type subsets to re-cluster in `subcluster`.
`gene_exploration`	Exploration CoreBlock	Genes / gene sets to score (AUCell) and plot in the exploration block, plus its `niche_column` and rank fraction.

!!! note A few one-key blocks are documented elsewhere for readability: integration (integrate_key) and extra_annotations (columns) are parameters in section 3; cluster_annotations is a file in section 2; and the colour blocks (sample_colors, annotation_colors, analysis.region_colors) are in section 4.

6. Advanced: Reproducibility and reusability

Even though we have ensured the highest reproducibility standards when creating SpaceBlocks, some steps are never 100% reproducible between systems (e.g. UMAP calculation, Leiden clustering).

We therefore provide features for minimal file sharing/storage that tighten the reproducibility gap.

SpaceBlocks allows you to input:

Externally assembled h5ad AnnData objects — run mode: decoupled and point contract_dir at the directory of pre-built contract h5ads. The heads are skipped; the core validates and analyses them directly.
Pre-computed clusters / annotations — set use_precomputed_clusters: true and precomputed_metadata_dir to reuse Leiden clusters and metadata; for niches, set spatial_niches.use_precomputed: true with spatial_niches.niche_dir.
Externally annotated data — set external_annotation.enabled: true with external_annotation.column, and choose whether to keep or discard unannotated barcodes downstream via external_annotation.keep_unannotated (see section 5).

These files are generated during the run, and can be shared with minimum effort to reproduce downstream results from raw data.

7. Example use case configurations

The commented config/config.yaml is the full template. The mode-specific keys that differ are:

Visium HD (mode: visiumhd)

mode: "visiumhd"
samples: "config/visiumhd_samples.csv"          # fastq dirs / slide / area per sample
spaceranger: "/path/to/spaceranger"
probe_set: "/path/to/probe_set.csv"
transcriptome: "/path/to/refdata-gex"
spaceranger_processing_outdir: "/path/to/sr_out"

Xenium 5K (mode: xenium5k)

mode: "xenium5k"
xenium5k:
  xenium_dir: "/path/to/xenium/{sample}"   # {sample} pattern to each bundle
  zarr_dir: ""                             # "" → spaceranger_processing_outdir
  qupath_pyramid_level: 3
  hires_pyramid_level: 3
  pixel_size_um: 0.2125

Atera (mode: atera, alpha)

mode: "atera"
atera:
  atera_dir: "/path/to/atera/{sample}/outs"
  zarr_dir: ""
  qupath_pyramid_level: 3
  hires_pyramid_level: 3
  pixel_size_um: 0.2125
  he_image: ""       # optional {sample} pattern; set with he_alignment
  he_alignment: ""   # optional {sample} pattern; set with he_image
  he_keypoints: ""   # optional {sample} pattern

MERSCOPE (mode: merscope)

mode: "merscope"
merscope:
  merscope_dir: "/path/to/merscope/{sample}"
  z_index: 3
  hires_pixel_size_um: 1.0
  channels: [DAPI, PolyT, Cellbound1, Cellbound2, Cellbound3]

Externally prepared data (mode: decoupled)

mode: "decoupled"
contract_dir: "/path/to/contract_h5ads"    # one <sample>.h5ad file per sample

All modes additionally set core_samples, post_processing_outdir, logdir, and the other required common keys in config/config.yaml; geojson_path is optional but strongly recommended.

8. Minimal example

mode: "visiumhd"
samples: "config/visiumhd_samples.csv"
core_samples: "config/core_samples.tsv"
geojson_path: "/path/to/geojson"
post_processing_outdir: "/path/to/results"
# ... see config/config.yaml for the full, commented template.

Start from the commented config/config.yaml shipped with the workflow and adjust the paths and sample sheets to your data.

You may next read the get started documentation and the public data end-to-end example runs.

Workflow parameters

The following table is automatically parsed from the workflow’s config.schema.y(a)ml file.

Parameter	Type	Description	Required	Default
samples	string	Path to the Visium HD head sample sheet (fastq dirs / slide / area per sample; mode visiumhd).
snakemake_cell_markers	string	TSV of canonical marker genes drawn on the Leiden diagnostic plots to guide manual annotation.	yes
probe_set	string	Path to the 10x probe-set CSV needed to run Space Ranger (mode visiumhd).
transcriptome	string	Path to the Space Ranger reference transcriptome (mode visiumhd).
spaceranger	string	Path to the locally installed spaceranger executable
xenium5k	[‘object’, ‘null’]	Xenium 5K head settings (used only when mode == “xenium5k”).
. xenium_dir	string	{sample} pattern to each Xenium output bundle.
. zarr_dir	string	Where {sample}.zarr stores are written (”” → spaceranger_processing_outdir).
. qupath_pyramid_level	integer	Pyramid level of the morphology image used for the QuPath composite TIFF.		3
. hires_pyramid_level	integer	Pyramid level embedded as the uns[‘spatial’] background image.		3
. pixel_size_um	number	Xenium pixel size in microns.		0.2125
atera	[‘object’, ‘null’]	Atera head settings (used only when mode == “atera”). ALPHA support — validated against the 10x WTA preview bundle, whose format is not final.
. atera_dir	string	{sample} pattern to each Atera outs/ bundle.
. zarr_dir	string	Where {sample}.zarr stores are written (”” -> spaceranger_processing_outdir).
. qupath_pyramid_level	integer	Pyramid level of the morphology image used for the QuPath composite TIFF.		3
. hires_pyramid_level	integer	Pyramid level embedded as the uns[“spatial”] background image. Also the grid the registered H&E background is resampled onto, when one is configured.		3
. pixel_size_um	number	Microns per full-resolution morphology pixel (experiment.xenium pixel_size).		0.2125
. he_image	string	OPTIONAL absolute {sample} pattern to the registered H&E OME-TIFF, which ships separately from the outs/ bundle. When set together with he_alignment, a second QuPath image is produced, region annotations may be drawn on either image, and the H&E becomes the embedded contract background.
. he_alignment	string	OPTIONAL absolute {sample} pattern to the 10x 3x3 he_alignment.csv mapping full-resolution H&E pixels onto full-resolution morphology pixels. Required whenever he_image is set.
. he_keypoints	string	OPTIONAL absolute {sample} pattern to the 10x keypoints.csv. Not required, but without it the H&E transform is applied unverified.
. he_pyramid_level	integer	Pyramid level of the H&E read for the QuPath TIFF and the background warp.		4
. he_residual_warn_px	number	Warn when the largest keypoint residual exceeds this many morphology pixels — the tripwire for a changed alignment convention.		50
merscope	[‘object’, ‘null’]	MERSCOPE (Vizgen MERFISH) head settings (used only when mode == “merscope”).
. merscope_dir	string	{sample} pattern to each MERSCOPE region directory (holds the two Vizgen CSVs and the images/ folder).
. z_index	integer	Mosaic z-plane used for the QuPath composite and embedded background (DAPI/PolyT always present).		3
. hires_pixel_size_um	number	Target microns-per-pixel of the downsampled background embedded in uns[“spatial”] and annotated in QuPath.		1.0
. channels	array	Mosaic stains to composite, in order; channels absent on disk are skipped (default DAPI, PolyT, Cellbound1-3).
cluster_annotations	string	Optional path to a TSV with cluster-to-cell-type annotations. Rows are cluster numbers, columns are sample names, values are cell-type labels. If missing or empty, DE and neighbourhood analyses are skipped.
per_sample_qc	string	Optional path to a TSV of per-sample QC filtering thresholds for preprocess_umap. First column = sample name; remaining columns any of min_counts, min_genes, min_cells, max_counts, max_pct_mt. Present values override the analysis.* defaults per sample, key-by-key; missing samples/columns fall back to config. Empty string disables overrides.
mode	string	A HEAD technology name (that head builds the contract h5ads in this run) or “decoupled” (the core consumes pre-existing contracts from contract_dir; head rules skipped; validation aborts if any core_samples sample is missing its contract). Extend the enum as new heads are added (e.g. xenium5k). “atera” is ALPHA support: the platform ships in H2 2026 and the public data is a preview whose output format 10x state will change at commercial release.		visiumhd
core_samples	string	Optional path to the CORE sample sheet (TSV; required column `sample` plus optional experimental-design columns). Authoritative sample list for the core; empty = derive from the head visiumhd_samples.csv. The `sample` value need not match obs[“sample”] in the h5ad (samples may be renamed during preparation).
contract_dir	string	Directory the core reads contract h5ads from. Empty = the per-sample output tree. In decoupled mode, set to the head’s output location.
sample_colors	[‘object’, ‘null’]	Optional colour palettes for core-sheet columns: column -> {value -> hex}.
integration	[‘object’, ‘null’]	Integration settings for integrate_samples.
. integrate_key	string	obs column Harmony corrects on (“sample” = per-sample).
extra_annotations	[‘object’, ‘null’]	core_samples.tsv columns to surface downstream as UMAP colourings, pseudobulk QC panels, and DE heatmap annotation tracks. Annotation-only (no DESeq2 covariate).
. columns	array	Columns to plot/annotate ([] = all non-sample columns).
geojson_path	string	Directory of per-sample QuPath region-annotation GeoJSONs.	yes
spaceranger_processing_outdir	string	Directory where the head writes heavy intermediates (Space Ranger tree / SpatialData zarr).	yes
post_processing_outdir	string	Analysis output root; holds the result folders for the run.	yes
logdir	string	Directory for per-rule logs and benchmarks.	yes
analysis
. min_counts	integer	Minimum total counts per cell (QC filter).		1
. min_cells	integer	Minimum number of cells a gene must be detected in (QC filter).		3
. min_genes	integer	Minimum number of genes per cell (QC filter).		100
. max_counts	integer	Optional upper bound on total counts per cell (omit to disable).
. max_pct_mt	number	Optional upper bound on percent mitochondrial counts (omit to disable).
. n_top_genes	integer	Number of highly variable genes to select.		5000
. n_neighbors	integer	Number of neighbours for the kNN graph.		10
. n_pcs	integer	Number of principal components used to build the neighbours graph.		30
. leiden_resolution	number	Single Leiden resolution used when not scanning a range.		0.6
. resolution_scan_min	number	Lowest Leiden resolution in the multi-resolution scan.		0.8
. resolution_scan_max	number	Highest Leiden resolution in the multi-resolution scan.		1.2
. resolution_scan_step	number	Step between Leiden resolutions in the scan.		0.2
. de_n_genes	integer	Number of top differential-expression marker genes reported per group.		10
. run_pseudobulk_de	boolean	Gate the optional R/DESeq2 pseudobulk_de step.		false
. run_leiden_analysis	boolean	Produce the per-resolution Leiden diagnostic plots. Optional (clustering itself happens in preprocess_umap); set false to skip, e.g. when overlaying external annotation.		true
. analysis_levels	array	Pseudobulk analysis levels (e.g. by_region, by_celltype_region).
. region_levels	array	Ordered region names (must match region_annotation values in the data).
. region_colors		region name -> hex colour.
. plot_dpi	integer	Default figure DPI.
ingest_ref	string	Optional reference h5ad for scanpy label transfer (ingest_ref rule) and the qc_sweep cell-type overlay. Empty string disables ingest.
ingest_ref_label_key	string	obs column in the ingest reference holding the cell-type label.
annotation_types	array	Annotation types analysed downstream (neighbourhood, pseudobulk). Defaults to [“tsv_annotation”] when omitted.
random_seed	integer	Global RNG seed.
use_precomputed_clusters	boolean	Reuse precomputed cluster metadata when available.
precomputed_metadata_dir	string	Directory of precomputed metadata_{sample}.tsv (with use_precomputed_clusters).
external_annotation	[‘object’, ‘null’]	Optional external cell-type annotation source.
. enabled	boolean	Enable overlaying external cell-type labels.		false
. column	string	obs/metadata column holding the external label.
. keep_unannotated	boolean	false → keep only externally-annotated cells and skip pipeline QC (external labels drive QC); true → normal QC, labels overlaid at annotation.		true
contract	[‘object’, ‘null’]	Semantic HEAD->CORE contract keys. `unfiltered_h5ad` and `outdir` are injected by the Snakefile after validation and are intentionally not defined here.
. sample_key	string	obs column holding the sample id.		sample
. spatial_key	string	obsm key holding the spatial coordinates.		spatial
. require_region	boolean	If true, a missing region_annotation is a hard validation failure.		false
. require_raw_counts	boolean	If true, validate that X holds non-negative integer raw counts.		true
. mito_prefix	array	Gene-name prefixes used to flag mitochondrial genes.
qc_sweep	[‘object’, ‘null’]	OPTIONAL pre-filtering QC diagnostic (target qc_sweep_all).
. ingest_enabled	boolean	Overlay ingest-reference cell types on the QC-sweep plots.		false
. dpi	integer	Figure resolution (DPI) for the QC-sweep plots.		300
. thresholds		Candidate cut-off LISTS per feature (min_genes/min_counts/max_counts/max_pct_mt).
. ingest_key	string	(Legacy; unused — qc_sweep reuses the top-level ingest_ref.)
. cell_id_key	string	(Legacy; unused.)
annotation_colors	[‘object’, ‘null’]	Cell-type colour palettes — annotation column -> {value -> hex}.
gene_exploration	[‘object’, ‘null’]	Gene/signature exploration settings (target explore_genes).
. queries	string	TSV of genes / gene sets to score (AUCell) and plot.
. annot_key	string	Annotation column used to colour the exploration plots.
. niche_column	string	obs column holding the spatial-niche label.
. aucell_max_rank_fraction	number	AUCell max rank, as a fraction of the ranked genes.
. dpi	integer	Figure resolution (DPI) for the exploration plots.		300
spatial_niches	[‘object’, ‘null’]	OPTIONAL cross-sample spatial-niche identification.
. enabled	boolean	Enable BANKSY spatial-niche detection.		false
. use_precomputed	boolean	Reuse precomputed niche assignments from niche_dir instead of recomputing.
. niche_dir	string	Directory of precomputed per-sample niche TSVs.
subcompartments	[‘object’, ‘null’]	Subcompartment definitions for the subcluster rule (name -> settings). Keys are the subcompartment names; each needs a non-empty `strings` list of cell types.
resources			yes

Linting and formatting

Linting results

/home/runner/work/snakemake-workflow-catalog/snakemake-workflow-catalog/.pixi/envs/default/lib/python3.13/site-packages/google/auth/transport/grpc.py:44: FutureWarning: grpcio < 1.83.0 does not support Post-Quantum Cryptography (PQC). Support for non-PQC environments is deprecated. In October 2026, google-auth will raise its minimum requirements to enforce grpcio >= 1.83.0. For more details on Google Cloud's post-quantum security migration, visit: https://cloud.google.com/security/resources/post-quantum-cryptography
  warnings.warn(
Using workflow specific profile profiles/default for setting default command line arguments.
[validate_input / decoupled] Missing contract h5ad for 3 sample(s) in the input directory:
  - sample1: /scratch/CBiB/soterino/smk_visiumhd_results/Samples/sample1.h5ad
  - sample2: /scratch/CBiB/soterino/smk_visiumhd_results/Samples/sample2.h5ad
  - sample3: /scratch/CBiB/soterino/smk_visiumhd_results/Samples/sample3.h5ad
Every sample in the core sheet must already have a contract present as <contract_dir>/<sample>.h5ad (mode: decoupled does not build them). Fix the sheet or contract_dir, or set mode to a head technology (e.g. visiumhd).