Build branch openpipeline_spatial/niche-compass with version niche-compass to openpipeline_spatial on branch niche-compass (9151204)

Build pipeline: openpipelines-bio.openpipeline-spatial.niche-compass-29shs Source commit: 9151204629 Source message: poc
2025-12-13 14:07:35 +00:00
parent 560dea5ec5
commit db66152ef1
105 changed files with 21553 additions and 1280 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -22,6 +22,8 @@

 * `convert/from_cosmx_to_h5mu`: Updated component to handle CosMx output bundles generated with AtoMx SIP versions < v1.3.2 (PR #25).

+* `nichecompass/gene_program_mask`: Added a component to create a prior knowledge gene program mask for NicheComnpass analysis (PR #27).
+
 # openpipeline_spatial 0.1.0

 ## NEW FUNCTIONALITY
--- a/resources_test_scripts/niche_analysis.sh
+++ b/resources_test_scripts/niche_analysis.sh
@@ -0,0 +1,51 @@
+#!/bin/bash
+
+set -eo pipefail
+
+# get the root of the directory
+REPO_ROOT=$(git rev-parse --show-toplevel)
+
+# ensure that the command below is run from the root of the repository
+cd "$REPO_ROOT"
+
+DIR="resources_test/niche"
+ID="nichecompass"
+
+# create tempdir
+MY_TEMP="${VIASH_TEMP:-/tmp}"
+TMPDIR=$(mktemp -d "$MY_TEMP/$ID-XXXXXX")
+function clean_up {
+  [[ -d "$TMPDIR" ]] && rm -r "$TMPDIR"
+}
+trap clean_up EXIT
+
+if [ ! -d "$DIR" ]; then
+    mkdir -p "$DIR"
+
+    orthologue_url="https://raw.githubusercontent.com/Lotfollahi-lab/nichecompass/refs/tags/0.3.2/data/gene_annotations/human_mouse_gene_orthologs.csv"
+    orthologue_file="human_mouse_gene_orthologs.csv"
+    wget "$orthologue_url" -O "$DIR/$orthologue_file"
+
+    enzymes_url="https://raw.githubusercontent.com/Lotfollahi-lab/nichecompass/refs/tags/0.3.2/data/gene_programs/metabolite_enzyme_sensor_gps/mouse_metabolite_enzymes.tsv"
+    enzymes_file="mouse_metabolite_enzymes.tsv"
+    wget "$enzymes_url" -O "$DIR/$enzymes_file"
+
+    sensors_url="https://raw.githubusercontent.com/Lotfollahi-lab/nichecompass/refs/tags/0.3.2/data/gene_programs/metabolite_enzyme_sensor_gps/mouse_metabolite_sensors.tsv"
+    sensors_file="mouse_metabolite_sensors.tsv"
+    wget "$sensors_url" -O "$DIR/$sensors_file" 
+fi
+
+gp_mask="prior_knowledge_gp_mask.json"
+viash run src/nichecompass/gene_program_mask/config.vsh.yaml -- \
+    --input_gene_orthologs_mapping_file "$DIR/$orthologue_file" \
+    --input_metabolite_enzymes "$DIR/$enzymes_file" \
+    --input_metabolite_sensors "$DIR/$sensors_file" \
+    --output "${DIR}/${gp_mask}"
+
+# Sync to S3
+aws s3 sync \
+    --profile di \
+    "$DIR" \
+    s3://openpipelines-bio/openpipeline_spatial/resources_test/niche \
+    --delete \
+    --dryrun
--- a/src/base/requirements/testworkflows_setup.yaml
+++ b/src/base/requirements/testworkflows_setup.yaml
@@ -0,0 +1,10 @@
+setup:
+  - type: apt
+    packages:
+      - procps
+      - git
+  - type: python
+    __merge__:
+      - /src/base/requirements/anndata_mudata.yaml
+      - /src/base/requirements/openpipeline_testutils.yaml
+      - /src/base/requirements/viashpy.yaml
--- a/src/convert/from_cosmx_to_spatialexperiment/test.R
+++ b/src/convert/from_cosmx_to_spatialexperiment/test.R
@@ -75,9 +75,8 @@ spe <- paste0(meta[["resources_dir"]], "/Lung5_Rep2_tiny")
 out_rds <- "output.rds"

 create_folder_archive <- function(
-  folder_path,
-  archive = "Lung5_Rep2_tiny.zip"
-) {
+    folder_path,
+    archive = "Lung5_Rep2_tiny.zip") {
  old_wd <- getwd()
  on.exit(setwd(old_wd))
  setwd(meta$resources_dir)
--- a/src/dataflow/obsp_block_concatenation/test.py
+++ b/src/dataflow/obsp_block_concatenation/test.py
--- a/src/neighbors/spatial_neighborhood_graph/config.vsh.yaml
+++ b/src/neighbors/spatial_neighborhood_graph/config.vsh.yaml
@@ -1,5 +1,5 @@
-name: neighbors
-namespace: spatial_neighborhood_graph
+name: spatial_neighborhood_graph
+namespace: neighbors
 scope: public
 description: Calculates a spatial neighborhood graph.

--- a/src/nichecompass/gene_program_mask/config.vsh.yaml
+++ b/src/nichecompass/gene_program_mask/config.vsh.yaml
@@ -0,0 +1,186 @@
+name: gene_program_mask
+namespace: nichecompass
+scope: public
+description: Generation of a prior knowledge gene program mask for NicheCompass.
+
+authors:
+  - __merge__: /src/authors/dorien_roosen.yaml
+    roles: [ maintainer ]
+
+argument_groups:
+  - name: Inputs
+    arguments: 
+      - name: "--input_gene_orthologs_mapping_file"
+        type: file
+        required: false
+        description: |
+          Path to a CSV file mapping human genes to mouse orthologs.
+          Required for the OmniPath and NicheNet masks if `--species mouse`.
+      - name: "--input_metabolite_enzymes"
+        type: file
+        required: false
+        description: |
+          Path to the MeBocost metabolite-enzymes TSV file.
+          Required for generating the MeBocost gene program mask.
+      - name: "--input_metabolite_sensors"
+        type: file
+        required: false
+        description: |
+          Path to the MeBocost metabolite-sensors TSV file.
+          Required for generating the MeBocost gene program mask.
+
+  - name: Parameters
+    arguments:
+      - name: "--species"
+        type: string
+        choices: ["human", "mouse"]
+        default: "human"
+        description: Species of the organism (human or mouse).
+      - name: "--create_omnipath_gene_program_mask"
+        type: boolean
+        default: true
+        description: Whether to create the OmniPath gene program mask.
+      - name: "--create_nichenet_gene_program_mask"
+        type: boolean
+        default: true
+        description: Whether to create the NicheNet gene program mask.
+      - name: "--create_mebocost_gene_program_mask"
+        type: boolean
+        default: true
+        description: Whether to create the MeBocost gene program mask.
+      - name: "--create_collectri_tf_gene_program_mask"
+        type: boolean
+        default: true
+        description: Whether to create the CollecTRI TF gene program mask.
+      - name: "--overlap_thresh_target_genes"
+        type: double
+        default: 1.0
+        min: 0.0
+        max: 1.0
+        description: |
+          The minimum ratio of target genes that need to overlap between a GP without source genes and another GP for the GP to be dropped.
+          Gene programs with different source genes are never combined or dropped.
+
+  - name: Omnipath Parameters
+    arguments:
+      - name: "--omnipath_min_curation_effort"
+        type: integer
+        default: 2
+        description: Minimum number of times an interaction has to be described in a paper and mentioned in a database to be included in the OmniPath gene programs.
+  
+  - name: NicheNet Parameters
+    arguments:
+      - name: "--nichenet_version"
+        type: string
+        choices: ["v1", "v2"]
+        default: "v2"
+        description: |
+          Version of the NicheNet ligand receptor network and ligand target gene regulatory potential matrix.
+          ´v2´ is an improved version of ´v1´, and has separate files for mouse and human.
+      - name: "--nichenet_keep_target_genes_ratio"
+        type: double
+        default: 1.0
+        description: |
+          Ratio of target genes that are kept compared to total target genes.
+          This ratio is applied over the entire matrix (not on gene program level), and determines the ´all_gps_score_keep_threshold´, which will be used to filter target genes according to their regulatory potential scores.
+      - name: "--nichenet_max_n_target_genes_per_gp"
+        type: integer
+        default: 250
+        description: |
+          Maximum number of target genes per gene program. If a gene program has more target genes than ´max_n_target_genes_per_gp´, only the ´max_n_target_genes_per_gp´ gene programs with the highest regulatory potential scores will be kept.
+          Default value is chosen based on MultiNicheNet specification (s. Browaeys, R. et al. MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data. bioRxiv (2023) doi:10.1101/2023.06.13.544751).
+
+  - name: Outputs
+    arguments:
+      - name: "--output"
+        type: file
+        direction: output
+        required: true
+        description: Path to the output gene program mask JSON file.
+        example: gp_mask.json
+      - name: "--output_omnipath_lr_network"
+        type: file
+        direction: output
+        required: false
+        description: Path to the output OmniPath ligand-receptor network CSV file.
+        example: omnipath_lr_network.csv
+      - name: "--output_nichenet_lr_network"
+        type: file
+        direction: output
+        required: false
+        description: Path to the output NicheNet ligand-receptor network CSV file.
+        example: nichenet_lr_network.csv
+      - name: "--output_nichenet_ligand_target_matrix"
+        type: file
+        direction: output
+        required: false
+        description: Path to the output NicheNet ligand-target gene regulatory potential matrix file.
+        example: nichenet_ligand_target_matrix.csv
+      - name: "--output_collectri_tf_network"
+        type: file
+        direction: output
+        required: false
+        description: Path to the output CollecTRI TF-target gene regulatory potential network CSV file.
+        example: collectri_tf_network.csv
+      - name: "--output_omnipath_gp_gene_count_distributions"
+        type: file
+        direction: output
+        required: false
+        description: Path to save the OmniPath gene program gene count distributions plot.
+        example: omnipath_gp_gene_count_distributions.svg
+      - name: "--output_nichenet_gp_gene_count_distributions"
+        type: file
+        direction: output
+        required: false
+        description: Path to save the NicheNet gene program gene count distributions plot.
+        example: nichenet_gp_gene_count_distributions.svg
+      - name: "--output_mebocost_gp_gene_count_distributions"
+        type: file
+        direction: output
+        required: false
+        description: Path to save the MeBocost gene program gene count distributions plot.
+        example: mebocost_gp_gene_count_distributions.svg
+      - name: "--output_collectri_tf_gp_gene_count_distributions"
+        type: file
+        direction: output
+        required: false
+        description: Path to save the CollecTRI TF gene program gene count distributions plot.
+        example: collectri_tf_gp_gene_count_distributions.svg
+
+resources:
+  - type: python_script
+    path: script.py
+  - path: /src/utils/setup_logger.py
+
+test_resources:
+  - type: python_script
+    path: test.py
+  - path: /resources_test/niche/
+
+engines:
+- type: docker
+  image: nvidia/cuda:12.4.1-cudnn-devel-ubuntu22.04
+  setup:
+    - type: apt
+      packages:
+        - libhdf5-dev
+        - python3-pip
+        - python3-dev
+        - python-is-python3
+    - type: docker
+      run: |
+        pip install torch --index-url https://download.pytorch.org/whl/cu124 \
+        && pip install pyg_lib torch-scatter torch-sparse -f https://data.pyg.org/whl/torch-2.6.0+cu124.html   
+    - type: python
+      packages:
+        - numpy<2
+        - nichecompass
+  test_setup:
+    - type: python
+      __merge__: [ /src/base/requirements/viashpy.yaml, .]
+
+runners:
+- type: executable
+- type: nextflow
+  directives:
+    label: [lowcpu, lowmem, lowdisk]
--- a/src/nichecompass/gene_program_mask/script.py
+++ b/src/nichecompass/gene_program_mask/script.py
@@ -0,0 +1,207 @@
+import os
+import sys
+import shutil
+import json
+
+from nichecompass.utils import (
+    extract_gp_dict_from_mebocost_ms_interactions,
+    extract_gp_dict_from_nichenet_lrt_interactions,
+    extract_gp_dict_from_omnipath_lr_interactions,
+    filter_and_combine_gp_dict_gps_v2,
+    extract_gp_dict_from_collectri_tf_network,
+)
+
+
+## VIASH START
+par = {
+    "species": "mouse",
+    "create_omnipath_gene_program_mask": True,
+    "create_nichenet_gene_program_mask": True,
+    "create_mebocost_gene_program_mask": True,
+    "create_collectri_tf_gene_program_mask": False,
+    # omnipath params
+    "input_gene_orthologs_mapping_file": "resources_test/niche/human_mouse_gene_orthologs.csv",
+    "omnipath_min_curation_effort": 2,
+    # nichenet params
+    "nichenet_version": "v2",
+    "nichenet_keep_target_genes_ratio": 1.0,
+    "nichenet_max_n_target_genes_per_gp": 250,
+    # mebocost_gene_program_mask
+    "input_metabolite_enzymes": "resources_test/niche/mouse_metabolite_enzymes.tsv",
+    "input_metabolite_sensors": "resources_test/niche/mouse_metabolite_sensors.tsv",
+    # filter and combine programs
+    "overlap_thresh_target_genes": 1.0,
+    # output paths
+    "output": "prior_knowledge_gene_program_mask.json",
+    "output_omnipath_lr_network": "omnipath_lr_network.csv",
+    "output_nichenet_lr_network": "nichenet_lr_network.csv",
+    "output_nichenet_ligand_target_matrix": "nichenet_ligand_target_matrix_v2_mouse.csv",
+    "output_collectri_tf_network": "collectri_tf_network.csv",
+    "output_omnipath_gp_gene_count_distributions": "omnipath_gp_gene_count_distributions.svg",
+    "output_nichenet_gp_gene_count_distributions": "nichenet_gp_gene_count_distributions.svg",
+    "output_mebocost_gp_gene_count_distributions": "mebocost_gp_gene_count_distributions.svg",
+    "output_collectri_tf_gp_gene_count_distributions": "collectri_tf_gp_gene_count_distributions.svg",
+}
+
+meta = {"temp_dir": "tmp/", "resources_dir": "src/utils/"}
+## VIASH END
+sys.path.append(meta["resources_dir"])
+from setup_logger import setup_logger
+
+logger = setup_logger()
+
+# Validate that inputs are provided correctly
+if not any(
+    [
+        par["create_omnipath_gene_program_mask"],
+        par["create_nichenet_gene_program_mask"],
+        par["create_mebocost_gene_program_mask"],
+        par["create_collectri_tf_gene_program_mask"],
+    ]
+):
+    raise ValueError("At least one gene program mask must be set to True")
+if (
+    par["create_omnipath_gene_program_mask"]
+    and par["species"] == "mouse"
+    and not par["input_gene_orthologs_mapping_file"]
+):
+    raise ValueError(
+        "For mouse species, a --input_gene_orthologs_mapping_file file must be provided for generating the omnipath mask."
+    )
+if (
+    par["create_nichenet_gene_program_mask"]
+    and par["species"] == "mouse"
+    and not par["input_gene_orthologs_mapping_file"]
+):
+    raise ValueError(
+        "For mouse species, a --input_gene_orthologs_mapping_file file must be provided for generating the nichenet mask."
+    )
+if par["create_mebocost_gene_program_mask"] and (
+    not par["input_metabolite_enzymes"] or not par["input_metabolite_sensors"]
+):
+    raise ValueError(
+        "For mebocost gene program mask, both --input_metabolite_enzymes and --input_metabolite_sensors files must be provided."
+    )
+
+# Assemble gene program dictionaries
+gp_dicts = []
+
+if par["create_omnipath_gene_program_mask"]:
+    logger.info("Generating Omnipath gene program mask...")
+
+    plot_gp_gene_count_distributions = (
+        True if par["output_omnipath_gp_gene_count_distributions"] else False
+    )
+    save_to_disk = True if par["output_omnipath_lr_network"] else False
+
+    omnipath_gp_dict = extract_gp_dict_from_omnipath_lr_interactions(
+        species=par["species"],
+        min_curation_effort=par["omnipath_min_curation_effort"],
+        load_from_disk=False,
+        save_to_disk=True,
+        lr_network_file_path=par["output_omnipath_lr_network"],
+        gene_orthologs_mapping_file_path=par["input_gene_orthologs_mapping_file"],
+        plot_gp_gene_count_distributions=plot_gp_gene_count_distributions,
+        gp_gene_count_distributions_save_path=par[
+            "output_omnipath_gp_gene_count_distributions"
+        ],
+    )
+
+    gp_dicts.append(omnipath_gp_dict)
+
+if par["create_nichenet_gene_program_mask"]:
+    logger.info("Generating NicheNet gene program mask...")
+
+    plot_gp_gene_count_distributions = (
+        True if par["output_nichenet_gp_gene_count_distributions"] else False
+    )
+    save_to_disk = (
+        True
+        if (
+            par["output_nichenet_lr_network"]
+            or par["output_nichenet_ligand_target_matrix"]
+        )
+        else False
+    )
+
+    nichenet_gp_dict = extract_gp_dict_from_nichenet_lrt_interactions(
+        species=par["species"],
+        version=par["nichenet_version"],
+        keep_target_genes_ratio=par["nichenet_keep_target_genes_ratio"],
+        max_n_target_genes_per_gp=par["nichenet_max_n_target_genes_per_gp"],
+        load_from_disk=False,
+        save_to_disk=save_to_disk,
+        lr_network_file_path=par["output_nichenet_lr_network"],
+        ligand_target_matrix_file_path=par["output_nichenet_ligand_target_matrix"],
+        gene_orthologs_mapping_file_path=par["input_gene_orthologs_mapping_file"],
+        plot_gp_gene_count_distributions=plot_gp_gene_count_distributions,
+        gp_gene_count_distributions_save_path=par[
+            "output_nichenet_gp_gene_count_distributions"
+        ],
+    )
+
+    gp_dicts.append(nichenet_gp_dict)
+
+if par["create_mebocost_gene_program_mask"]:
+    logger.info("Generating MeBocost gene program mask...")
+
+    shutil.copy2(
+        par["input_metabolite_enzymes"],
+        os.path.join(meta["temp_dir"], f"{par['species']}_metabolite_enzymes.tsv"),
+    )
+    shutil.copy2(
+        par["input_metabolite_sensors"],
+        os.path.join(meta["temp_dir"], f"{par['species']}_metabolite_sensors.tsv"),
+    )
+    plot_gp_gene_count_distributions = (
+        True if par["output_mebocost_gp_gene_count_distributions"] else False
+    )
+
+    mebocost_gp_dict = extract_gp_dict_from_mebocost_ms_interactions(
+        dir_path=meta["temp_dir"],
+        species=par["species"],
+        plot_gp_gene_count_distributions=plot_gp_gene_count_distributions,
+        gp_gene_count_distributions_save_path=par[
+            "output_mebocost_gp_gene_count_distributions"
+        ],
+    )
+
+    gp_dicts.append(mebocost_gp_dict)
+
+if par["create_collectri_tf_gene_program_mask"]:
+    logger.info("Generating CollecTRI TF gene program mask...")
+
+    plot_gp_gene_count_distributions = (
+        True if par["output_collectri_tf_gp_gene_count_distributions"] else False
+    )
+    save_to_disk = True if par["output_collectri_tf_network"] else False
+
+    collectri_gp_dict = extract_gp_dict_from_collectri_tf_network(
+        species=par["species"],
+        save_to_disk=save_to_disk,
+        tf_network_file_path=par["output_collectri_tf_network"],
+        plot_gp_gene_count_distributions=plot_gp_gene_count_distributions,
+        gp_gene_count_distributions_save_path=par[
+            "output_collectri_tf_gp_gene_count_distributions"
+        ],
+    )
+
+    gp_dicts.append(collectri_gp_dict)
+
+# Filter and combine GPs
+assert len(gp_dicts) > 0, "No gene program dictionaries were created."
+
+combined_gp_dict = filter_and_combine_gp_dict_gps_v2(
+    gp_dicts,
+    overlap_thresh_target_genes=par["overlap_thresh_target_genes"],
+    verbose=True,
+)
+
+logger.info("Gene program mask generation completed.")
+logger.info(
+    f"Number of gene programs after filtering and combining: {len(combined_gp_dict)}."
+)
+
+logger.info(f"Saving combined gene program mask to: {par['output']}")
+with open(par["output"], "w") as f:
+    json.dump(combined_gp_dict, f)
--- a/src/nichecompass/gene_program_mask/test.py
+++ b/src/nichecompass/gene_program_mask/test.py
@@ -0,0 +1,132 @@
+import pytest
+
+import json
+
+## VIASH START
+meta = {
+    "executable": "./target/executable/nichecompass/gene_program_mask/gene_program_mask",
+    "resources_dir": "./resources_test/niche/",
+}
+## VIASH END
+
+import sys
+
+sys.path.append(meta["resources_dir"])
+
+ortholog_file = f"{meta['resources_dir']}/niche/human_mouse_gene_orthologs.csv"
+enzymes_file = f"{meta['resources_dir']}/niche/mouse_metabolite_enzymes.tsv"
+sensors_file = f"{meta['resources_dir']}/niche/mouse_metabolite_sensors.tsv"
+
+
+def test_simple_execution(run_component, tmp_path):
+    output = tmp_path / "output.json"
+
+    args = [
+        "--input_gene_orthologs_mapping_file",
+        ortholog_file,
+        "--input_metabolite_enzymes",
+        enzymes_file,
+        "--input_metabolite_sensors",
+        sensors_file,
+        "--species",
+        "mouse",
+        "--output",
+        output,
+    ]
+
+    run_component(args)
+
+    # check files
+    assert output.is_file(), "Output file does not exist"
+
+    # Read gene program mask
+    with open(output, "r") as f:
+        gp_mask = json.load(f)
+
+    expected_gp_keys = [
+        "igand_receptor_GP",
+        "ligand_receptor_target_gene_GP",
+        "metabolite_enzyme_sensor_GP",
+        "TF_target_genes_GP",
+        "combined_GP",
+    ]
+    matching_gp = []
+    for key in expected_gp_keys:
+        assert any(key in gp for gp in gp_mask.keys()), (
+            f"No gene programs containing '{key}' found"
+        )
+
+        gp = next(gp for gp in gp_mask.keys() if key in gp)
+        matching_gp.append(gp)
+
+    for gp in matching_gp:
+        expected_keys = [
+            "sources",
+            "targets",
+            "sources_categories",
+            "targets_categories",
+        ]
+        assert all([key in gp_mask[gp] for key in expected_keys]), (
+            f"Gene program {gp} is missing expected keys"
+        )
+
+
+def test_outputs(run_component, tmp_path):
+    output = tmp_path / "output.json"
+    omnipath_lr = tmp_path / "omnipath_lr_network.tsv"
+    nichenet_lr = tmp_path / "nichenet_lr_network.tsv"
+    nichenet_lt = tmp_path / "nichenet_ligand_target_matrix.csv"
+    collectri_tf = tmp_path / "output_collectri_tf_network.csv"
+    omnipath_distr = tmp_path / "omnipath_distr.svg"
+    nichenet_distr = tmp_path / "nichenet_distr.svg"
+    mebocost_distr = tmp_path / "mebocost_distr.svg"
+    collectri_distr = tmp_path / "collectri_distr.svg"
+
+    args = [
+        "--input_gene_orthologs_mapping_file",
+        ortholog_file,
+        "--input_metabolite_enzymes",
+        enzymes_file,
+        "--input_metabolite_sensors",
+        sensors_file,
+        "--species",
+        "mouse",
+        "--output",
+        output,
+        "--output_omnipath_lr_network",
+        omnipath_lr,
+        "--output_nichenet_lr_network",
+        nichenet_lr,
+        "--output_nichenet_ligand_target_matrix",
+        nichenet_lt,
+        "--output_collectri_tf_network",
+        collectri_tf,
+        "--output_omnipath_gp_gene_count_distributions",
+        omnipath_distr,
+        "--output_nichenet_gp_gene_count_distributions",
+        nichenet_distr,
+        "--output_mebocost_gp_gene_count_distributions",
+        mebocost_distr,
+        "--output_collectri_tf_gp_gene_count_distributions",
+        collectri_distr,
+    ]
+
+    run_component(args)
+
+    expected_outputs = [
+        omnipath_lr,
+        nichenet_lr,
+        nichenet_lt,
+        collectri_tf,
+        omnipath_distr,
+        nichenet_distr,
+        mebocost_distr,
+        collectri_distr,
+    ]
+
+    for output in expected_outputs:
+        assert output.is_file(), f"Expected output file {output} does not exist"
+
+
+if __name__ == "__main__":
+    sys.exit(pytest.main([__file__]))
--- a/src/nichecompass/nichecompass/config.vsh.yaml
+++ b/src/nichecompass/nichecompass/config.vsh.yaml
@@ -42,30 +42,6 @@ argument_groups:
        multiple: true
        description: "Keys of the adata.obs fields to use as covariates."

-  - name: "Spatial Neighbors Calculation"
-    arguments:
-      - name: "--coord_type"
-        type: string
-        choices: ["generic", "grid"]
-        description: |
-          Type of coordinate system. Valid options are:
-          `grid` - grid coordinates.
-          `generic` - generic coordinates.
-          If not provided, `grid` is used if `--input_obsm_spatial_coords` is in --input .uns with `--n_neighs` = 6 (Visium), otherwise `generic` is used.
-      - name: "--n_spatial_neighbors"
-        type: integer
-        default: 6
-        description: |
-          Depending on `--coord_type`:
-          `grid` - number of neighboring tiles.
-          `generic` - number of neighborhoods for non-grid data. Only used when `--delaunay False`.
-      - name: "--delaunay"
-        type: boolean
-        default: false
-        description: |
-          Whether to use Delaunay triangulation to determine spatial neighborhood graph.
-          Only used when `--coord_type generic`.
-
  - name: Gene Program Mask 
    arguments:
      - name: "--min_genes_per_gp"
@@ -416,9 +392,9 @@ argument_groups:
        default: nichecompass_active_gp_names
        description: |
          Key of the uns field where the active gene program names will be stored.
-      - name: "--output_uns_gene_index"
+      - name: "--output_uns_genes_index"
        type: string
-        default: nichecompass_gene_idx
+        default: nichecompass_genes_idx
        description: |
          Key of the uns field where the index of a concatenated vector of target and source genes that are in the gene program masks will be stored.
      - name: "--output_uns_target_genes_index"
@@ -447,6 +423,7 @@ argument_groups:
        default: nichecompass_agg_weights
        description: |
          Key of the obsp field where the aggregation weights of the node label aggregator will be stored.
+    __merge__: [., /src/base/h5_compression_argument.yaml]

 resources:
  - type: python_script
--- a/src/nichecompass/nichecompass/script.py
+++ b/src/nichecompass/nichecompass/script.py
@@ -9,7 +9,7 @@ from torch.cuda import is_available as cuda_is_available
 ## VIASH START
 par = {
    # Inputs
-    "input": "resources_test/cosmx/Lung5_Rep2_tiny.h5mu",
+    "input": "work/8c/d3f8f50ac967abac81eabcda42798e/_viash_par/input_1/merged.obsp_block_concatenation.output.h5mu",
    "modality": "rna",
    "layer": None,
    "input_gp_mask": "resources_test/niche/prior_knowledge_gp_mask.json",
@@ -98,21 +98,19 @@ logger.info("GPU enabled? %s", use_gpu)
 ## Read in data
 adata = mu.read_h5ad(par["input"], mod=par["modality"])

-# ## Compute spatial neighbor graph
-# logger.info("Computing spatial neighbor graph...")
-# # Compute connectivities and distances
-# sq.gr.spatial_neighbors(
-#     adata,
-#     coord_type=par["coord_type"],
-#     spatial_key=par["input_obsm_spatial_coords"],
-#     n_neighs=par["n_spatial_neighbors"],
-#     delaunay=par["delaunay"],
-# )
-
-# # Making the connectivity matrix symmetric
-# adata.obsp["spatial_connectivities"] = adata.obsp["spatial_connectivities"].maximum(
-#     adata.obsp["spatial_connectivities"].T
-# )
+# Counts need to be float32 to be processed by nichecompass model
+# See https://discuss.pytorch.org/t/runtimeerror-mat1-and-mat2-must-have-the-same-dtype/166759
+counts_dtype = (
+    adata.layers[par["layer"]].dtype if par["layer"] is not None else adata.X.dtype
+)
+if counts_dtype != "float32":
+    logger.info(
+        f"Converting count data to float32 from {counts_dtype} for model compatibility..."
+    )
+    if par["layer"] is not None:
+        adata.layers[par["layer"]] = adata.layers[par["layer"]].astype("float32")
+    else:
+        adata.X = adata.X.astype("float32")

 ## Add GP mask to data
 logger.info("Adding prior knowledge gene program mask to data...")
@@ -125,7 +123,7 @@ add_gps_from_gp_dict_to_adata(
    gp_targets_mask_key=par["output_varm_gp_targets_mask"],
    gp_sources_mask_key=par["output_varm_gp_sources_mask"],
    gp_names_key=par["output_uns_gp_names"],
-    genes_idx_key=par["output_uns_gene_index"],
+    genes_idx_key=par["output_uns_genes_index"],
    target_genes_idx_key=par["output_uns_target_genes_index"],
    source_genes_idx_key=par["output_uns_source_genes_index"],
    min_genes_per_gp=par["min_genes_per_gp"],
@@ -148,12 +146,12 @@ model = NicheCompass(
    gp_sources_mask_key=par["output_varm_gp_sources_mask"],
    latent_key=par["output_obsm_embedding"],
    cat_covariates_keys=par["input_obs_covariates"],
-    cat_covariates_no_edges=par["covariates_edges"],
+    cat_covariates_no_edges=par["covariate_edges"],
    cat_covariates_embeds_keys=par["output_uns_covariate_embeddings"],
-    cat_covariates_embeds_injection_layers=par["covariate_embedding_injection_layers"],
-    gene_idx_key=par["output_uns_gene_index"],
-    target_gene_idx_key=par["output_uns_target_genes_index"],
-    source_gene_idx_key=par["output_uns_source_genes_index"],
+    cat_covariates_embeds_injection=par["covariate_embedding_injection_layers"],
+    genes_idx_key=par["output_uns_genes_index"],
+    target_genes_idx_key=par["output_uns_target_genes_index"],
+    source_genes_idx_key=par["output_uns_source_genes_index"],
    recon_adj_key=par["output_obsp_reconstructed_adj_edge_proba"],
    agg_weights_key=par["output_obsp_agg_weights"],
    include_edge_recon_loss=par["include_edge_recon_loss"],
@@ -174,7 +172,6 @@ model = NicheCompass(
    encoder_use_bn=par["encoder_use_bn"],
    dropout_rate_encoder=par["dropout_rate_encoder"],
    dropout_rate_graph_decoder=par["dropout_rate_graph_decoder"],
-    cat_covariates_cats=par["cat_covariates_cats"],
    n_addon_gp=par["n_addon_gp"],
    cat_covariates_embeds_nums=par["cat_covariates_embeds_nums"],
    seed=par["random_state"],
@@ -212,6 +209,6 @@ model.train(
 ## Save model and data
 logger.info("Saving NicheCompass model and data...")
 mdata = mu.MuData({par["modality"]: adata})
-mdata.write_h5mu(par["output"])
+mdata.write_h5mu(par["output"], compression=par["output_compression"])

 model.save(par["output_model"], save_adata=False)
--- a/src/nichecompass/nichecompass/test.py
+++ b/src/nichecompass/nichecompass/test.py
@@ -1,5 +1,6 @@
 import pytest
 import mudata as mu
+import sys

 ## VIASH START
 meta = {
@@ -24,13 +25,16 @@ def test_simple_execution_xenium(run_component, tmp_path):
            gp_mask,
            "--n_epochs",
            "1",
-            "n_epochs_all_gps",
+            "--n_epochs_all_gps",
            "0",
-            "n_epochs_no_edge_recon",
+            "--n_epochs_no_edge_recon",
            "0",
-            "n_epochs_no_cat_covariates_contrastive",
-            "0--output",
+            "--n_epochs_no_cat_covariates_contrastive",
+            "0",
+            "--output",
            str(output),
+            "--output_model",
+            "test_model",
            "--output_compression",
            "gzip",
        ]
@@ -50,17 +54,15 @@ def test_simple_execution_xenium(run_component, tmp_path):
        "nichecompass_gp_names",
        "nichecompass_active_gp_names",
    ]
-    assert all([uns in expected_uns_keys for uns in adata.uns.keys()])
+    assert all([uns in adata.uns.keys() for uns in expected_uns_keys]), (
+        f"Expected uns keys: {expected_uns_keys}, found: {list(adata.uns.keys())}"
+    )
    assert len(adata.uns["nichecompass_gp_names"]) > len(
        adata.uns["nichecompass_active_gp_names"]
    ), "Expected less active GP names than total GP names"
-    assert adata.uns["nichecompass_genes_idx"] == (
-        adata.uns["nichecompass_source_genes_idx"]
-        + adata.uns["nichecompass_target_genes_idx"]
-    ), "Expected genes idx to be union of source and target genes idx"

    expected_obsm_keys = ["nichecompass_latent"]
-    assert all([obsm in expected_obsm_keys for obsm in adata.obsm.keys()]), (
+    assert all([obsm in adata.obsm.keys() for obsm in expected_obsm_keys]), (
        "Not all expected obsm keys found"
    )
    assert all(adata.obsm[obsm].dtype.kind == "f" for obsm in expected_obsm_keys), (
@@ -73,7 +75,7 @@ def test_simple_execution_xenium(run_component, tmp_path):
        "nichecompass_gp_sources_categories",
        "nichecompass_gp_targets_categories",
    ]
-    assert all([varm in expected_varm_keys for varm in adata.varm.keys()]), (
+    assert all([varm in adata.varm.keys() for varm in expected_varm_keys]), (
        "Not all expected varm keys found"
    )
    assert (
@@ -83,4 +85,4 @@ def test_simple_execution_xenium(run_component, tmp_path):


 if __name__ == "__main__":
-    pytest.main([__file__])
+    sys.exit(pytest.main([__file__]))
--- a/src/workflows/niche/nichecompass_leiden/config.vsh.yaml
+++ b/src/workflows/niche/nichecompass_leiden/config.vsh.yaml
@@ -0,0 +1,371 @@
+name: "nichecompass_leiden"
+namespace: "workflows/niche"
+scope: "public"
+description: "A pipeline to compute the spatial neighborhood graph, perform nichecompass embedding followed by Leiden clustering."
+authors:
+  - __merge__: /src/authors/dorien_roosen.yaml
+    roles: [ author, maintainer ]
+  - __merge__: /src/authors/weiwei_schultz.yaml
+    roles: [ contributor ]
+info:
+  test_dependencies:
+    - name: nichecompass_leiden_test
+      namespace: test_workflows/niche
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: "--id"
+        required: true
+        type: string
+        description: ID of the sample.
+        example: foo
+      - name: "--input"
+        alternatives: [-i]
+        description: Path to the sample.
+        required: true
+        example: input.h5mu
+        type: file
+      - name: "--input_gp_mask"
+        type: file
+        required: true
+        description: |
+          JSON file containing a nested dictionary containing the gene programs,
+          with keys being gene program names and values being dictionaries with keys `targets` and `sources`,
+          where `targets` contains a list of the names of genes in the gene program for the reconstruction of the gene expression of the node itself (receiving node)
+          and `sources` contains a list of the names of genes in the gene program for the reconstruction of the gene expression of the node's neighbors (transmitting nodes).
+        example: prior_knowledge_gp_mask.json
+      - name: "--modality"
+        description: Which modality to process.
+        type: string
+        default: "rna"
+        required: false
+      - name: "--layer"
+        description: "Use specified layer for calculation of qc metrics. If not specified, adata.X is used."
+        type: string
+        example: "raw_counts"
+        required: false
+      - name: "--input_obs_covariates"
+        type: string
+        multiple: true
+        default: ["sample_id"]
+        description: "Keys of the adata.obs fields to use as covariates."
+      - name: "--input_obsm_spatial_coords"
+        type: string
+        default: "spatial"
+        description: "Key in adata.obsm where spatial coordinates are stored"
+
+  - name: "Sample ID options"
+    description: |
+      Options for adding the id to .obs on the MuData object. Having a sample 
+      id present in a requirement of several components for this pipeline.
+    arguments:
+      - name: "--include_sample_as_covariate"
+        description: |
+          Whether to include the sample information as a categorical covariate for the 
+          NicheCompass model.
+        type: boolean
+        default: true
+      - name: "--add_id_to_obs"
+        description: "Add the value passed with --id to .obs."
+        type: boolean
+        default: true
+      - name: --add_id_obs_output
+        description: |
+          .Obs column to add the sample IDs to. Required and only used when 
+          --add_id_to_obs is set to 'true'
+        type: string
+        default: "sample_id"
+      - name: "--add_id_make_observation_keys_unique"
+        type: boolean
+        description: |
+          Join the id to the .obs index (.obs_names). 
+          Only used when --add_id_to_obs is set to 'true'.
+        default: true
+
+  - name: "Spatial Neighbors Calculation"
+    description: |
+      Options for the calculation of the spatial neighborhood graph.
+    arguments:
+      - name: "--coord_type"
+        type: string
+        choices: ["generic", "grid"]
+        description: |
+          Type of coordinate system provided by `--input_obsm_spatial_coords`. Valid options are:
+          `grid` - grid coordinates.
+          `generic` - generic coordinates.
+          If not provided, `grid` is used if `--input_obsm_spatial_coords` is in --input .uns with `--n_neighs` = 6 (Visium), otherwise `generic` is used.
+      - name: "--n_spatial_neighbors"
+        type: integer
+        default: 6
+        description: |
+          Depending on `--coord_type`:
+          `grid` - number of neighboring tiles.
+          `generic` - number of neighborhoods for non-grid data. Only used when `--delaunay False`.
+      - name: "--delaunay"
+        type: boolean
+        default: false
+        description: |
+          Whether to use Delaunay triangulation to determine spatial neighborhood graph.
+          Only used when `--coord_type generic`.
+  
+  - name: Gene Program Mask 
+    description: Options for filtering gene programs based on the number of genes available in the data.
+    arguments:
+      - name: "--min_genes_per_gp"
+        type: integer
+        default: 1
+        min: 0
+        description: |
+          Minimum number of genes in a gene program inluding both target and source genes that need to be available in the input data (gene expression has been probed) for a gene program not to be discarded.
+      - name: "--min_source_genes_per_gp"
+        type: integer
+        default: 0
+        min: 0
+        description: |
+          Minimum number of source genes in a gene program that need to be available in the input data (gene expression has been probed) for a gene program not to be discarded.
+      - name: "--min_target_genes_per_gp"
+        type: integer
+        default: 0
+        min: 0
+        description: |
+          Minimum number of target genes in a gene program that need to be available in the input data (gene expression has been probed) for a gene program not to be discarded.
+      - name: "--max_genes_per_gp"
+        type: integer
+        min: 1
+        description: |
+          Maximum number of genes in a gene program inluding both target and source genes that can be available in the input data (gene expression has been probed) for a gene program not to be discarded.
+      - name: "--max_source_genes_per_gp"
+        type: integer
+        min: 1
+        description: |
+          Maximum number of source genes in a gene program that can be available in the input data (gene expression has been probed) for a gene program not to be discarded.
+      - name: "--max_target_genes_per_gp"
+        type: integer
+        min: 1
+        description: |
+          Maximum number of target genes in a gene program that can be available in the input data (gene expression has been probed) for a gene program not to be discarded.
+      - name: "--filter_genes_not_in_masks"
+        type: boolean_true
+        description: |
+          Whether to remove the genes that are not in the gp masks from the input data.
+
+  - name: NicheCompass Model Architecture
+    description: Options for the NicheCompass model architecture.
+    arguments:
+      - name: "--covariate_edges"
+        type: boolean
+        multiple: true
+        description: |
+          List of booleans that indicate whether there can be edges between different categories of the categorical covariates.
+          If this is `True` for a specific categorical covariate, this covariate will be excluded from the edge reconstruction loss.
+          Needs to match the length and order of `--input_obs_covariates`.
+      - name: "--gene_expr_recon_dist"
+        type: string
+        choices: ["nb", "zinb"]
+        default: "nb"
+        description: |
+          The distribution used for gene expression reconstruction. 
+          If `nb`, uses a negative binomial distribution. 
+          If `zinb`, uses a zero-inflated negative binomial distribution.
+      - name: "--log_variational"
+        type: boolean
+        default: true
+        description: |
+          Whether to transform x by log(x+1) prior to encoding for numerical stability (not for normalization).
+      - name: "--node_label_method"
+        type: string
+        choices: ["one-hop-norm", "two-hop-norm", "one-hop-attention"]
+        default: "one-hop-norm"
+        description: |
+          Node label method that will be used for omics reconstruction.
+          If `one-hop-sum`, uses a concatenation of the node's input features with the sum of the input features of all nodes in the node's one-hop neighborhood.
+          If `one-hop-norm`, uses a concatenation of the node's input features with the node's one-hop neighbors input features normalized as per Kipf, T. N. & Welling, M. Semi-Supervised Classification with Graph Convolutional Networks. arXiv [cs.LG] (2016).
+          If `one-hop-attention`, uses a concatenation of the node's input features with the node's one-hop neighbors input features weighted by an attention mechanism.
+      - name: "--active_gp_thresh_ratio"
+        type: double
+        default: 0.1
+        min: 0.0
+        max: 1.0
+        description: |
+          Ratio that determines which gene programs are considered active and are used in the latent representation after model training.
+          All inactive gene programs will be dropped during model training after a determined number of epochs.
+          Aggregations of the absolute values of the gene weights of the gene expression decoder per gene program are calculated.
+          The maximum value, i.e. the value of the gene program with the highest aggregated value will be used as a benchmark and all gene programs whose aggregated value is smaller than `--active_gp_thresh_ratio` times this maximum value will be set to inactive.
+          If set to 0, all gene programs will be considered active.
+      - name: "--active_gp_type"
+        type: string
+        choices: ["mixed", "separate"]
+        default: "separate"
+        description: |
+          Type to determine active gene programs. 
+          Can be `mixed`, in which case active gene programs are determined across prior and add-on gene programs jointly,
+          or `separate` in which case they are determined separately for prior and add-on gene programs.
+      - name: "--n_addon_gp"
+        type: integer
+        default: 100
+        min: 0
+        description: |
+          Number of addon gene programs (i.e. gene programs that are not included in masks but can be learned de novo).
+      - name: "--cat_covariates_embeds_nums"
+        type: integer
+        multiple: true
+        description: |
+          Number of embedding nodes for all categorical covariates.
+          Must be the same length as `--input_obs_covariates`.
+      - name: "--random_state"
+        default: 0
+        type: integer
+        min: 0
+        description: |
+          Random seed for reproducibility.
+
+  - name: NicheCompass Training Parameters
+    description: Options for training the NicheCompass model.
+    arguments:
+      - name: "--n_epochs"
+        type: integer
+        min: 1
+        default: 100
+        description: Number of training epochs
+      - name: "--n_epochs_all_gps"
+        type: integer
+        min: 0
+        default: 25
+        description: |
+          Number of epochs during which all gene programs are used for model training.
+          After that only active gene programs are retained.
+      - name: "--n_epochs_no_edge_recon"
+        type: integer
+        default: 0
+        min: 0
+        description: |
+          Number of epochs during which the edge reconstruction loss is excluded from backpropagation for pretraining using the other loss components.
+      - name: "--n_epochs_no_cat_covariates_contrastive"
+        type: integer
+        default: 5
+        min: 0
+        description: |
+          Number of epochs during which the categorical covariates contrastive loss is excluded from backpropagation for pretraining using the other loss components.
+      - name: "--lr"
+        type: double
+        default: 0.001
+        min: 0.0
+        max: 1.0
+        description: Learning rate
+      - name: "--weight_decay"
+        type: double
+        default: 0.001
+        description: Weight decay (L2 penalty).
+      - name: "--edge_val_ratio"
+        type: double
+        default: 0.1
+        min: 0.0
+        max: 1.0
+        description: |
+          Fraction of the data that is used as validation set on edge-level. The rest of the data will be used as training set on edge-level.
+      - name: "--node_val_ratio"
+        type: double
+        default: 0.1
+        min: 0.0
+        max: 1.0
+        description: |
+          Fraction of the data that is used as validation set on node-level. The rest of the data will be used as training set on node-level.
+      - name: "--edge_batch_size"
+        type: integer
+        min: 1
+        default: 256
+        description: |
+          Batch size for the edge-level dataloaders.
+      - name: "--node_batch_size"
+        type: integer
+        min: 1
+        description: |
+          Batch size for the node-level dataloaders.
+          If not provided, is automatically determined based on `--edge_batch_size`.
+      - name: "--n_sampled_neighbors"
+        type: integer
+        default: -1
+        min: -1
+        description: |
+          Number of neighbors that are sampled during model training from the spatial neighborhood graph.
+          If set to -1, all direct neighbors are included.
+
+  - name: Clustering options
+    arguments:
+      - name: "--obs_cluster"
+        type: string
+        description: |
+          Prefix for the .obs keys under which to add the cluster labels. Newly created columns in .obs will 
+          be created from the specified value for '--obs_cluster' suffixed with an underscore and one of the resolutions
+          resolutions specified in '--leiden_resolution'.
+        default: "nichecompass_leiden"
+      - name: "--leiden_resolution"
+        type: double
+        description: Control the coarseness of the clustering. Higher values lead to more clusters.
+        default: [1]
+        multiple: true
+
+  - name: Umap options
+    arguments:
+      - name: "--obsm_umap"
+        type: string
+        default: "X_leiden_nichecompass_umap"
+        required: false
+        description: "In which .obsm slot to store the resulting UMAP embedding."
+
+  - name: Neighbour calculation
+    arguments:
+      - name: "--uns_neighbors"
+        type: string
+        default: nichecompass_neighbors
+        description: In which .uns slot to store various neighbor output objects.
+      - name: "--obsp_neighbor_distances"
+        type: string
+        default: "nichecompass_distances"
+        description: "In which .obsp slot to store the distance matrix between the resulting neighbors."
+      - name: "--obsp_neighbor_connectivities"
+        type: string
+        default: "nichecompass_connectivities"
+        description: "In which .obsp slot to store the connectivities matrix between the resulting neighbors."
+
+  - name: "Outputs"
+    arguments:
+      - name: "--output"
+        type: file
+        required: true
+        direction: output
+        description: Destination path to the output.
+        example: output.h5mu
+      - name: "--output_model"
+        type: file
+        required: true
+        direction: output
+        description: Directory to save the trained NicheCompass model.
+      - name: "--output_obsm_embedding"
+        type: string
+        default: nichecompass_latent
+        description: |
+          Key of the obsm field where the latent / gene program representation of active gene programs will be stored after NicheCompass model training.
+
+dependencies:
+  - name: dataflow/obsp_block_concatenation
+  - name: neighbors/spatial_neighborhood_graph
+  - name: nichecompass/nichecompass
+  - name: metadata/add_id
+    repository: openpipeline
+  - name: workflows/multiomics/neighbors_leiden_umap
+    repository: openpipeline
+
+resources:
+  - type: nextflow_script
+    path: main.nf
+    entrypoint: run_wf
+test_resources:
+  - type: nextflow_script
+    path: test.nf
+    entrypoint: test_wf
+  - path: /resources_test/xenium/xenium_tiny.h5mu
+  - path: /resources_test/cosmx/Lung5_Rep2_tiny.h5mu
+  - path: /resources_test/niche/prior_knowledge_gp_mask.json
+runners:
+  - type: nextflow
--- a/src/workflows/niche/nichecompass_leiden/integration_test.sh
+++ b/src/workflows/niche/nichecompass_leiden/integration_test.sh
@@ -0,0 +1,16 @@
+#!/bin/bash
+
+# get the root of the directory
+REPO_ROOT=$(git rev-parse --show-toplevel)
+
+# ensure that the command below is run from the root of the repository
+cd "$REPO_ROOT"
+
+nextflow \
+  run . \
+  -main-script src/workflows/niche/nichecompass_leiden/test.nf \
+  -entry test_wf \
+  -resume \
+  -profile docker,no_publish \
+  -c src/workflows/utils/labels_ci.config \
+  -c src/workflows/utils/integration_tests.config
--- a/src/workflows/niche/nichecompass_leiden/main.nf
+++ b/src/workflows/niche/nichecompass_leiden/main.nf
@@ -0,0 +1,162 @@
+workflow run_wf {
+  take:
+    input_ch
+
+  main:
+    output_ch = input_ch
+
+    | map { id, state ->
+      [id, state + [
+        workflow_output: state.output,
+        _meta: [join_id: id]
+      ]]
+    }
+    // If requested, add the id of the events (samples) to a column in .obs. 
+    // Also allows to make .obs_names (the .obs index) unique, by prefixing the values with an unique id per .h5mu file.
+    // The latter is usefull to avoid duplicate observations during concatenation.
+    | add_id.run(
+      filter: {id, state -> state.add_id_to_obs },
+      fromState: {id, state -> 
+        def newState = [
+          "input": state.input,
+          "input_id": id,
+          "make_observation_keys_unique": state.add_id_make_observation_keys_unique,
+          "obs_output": state.add_id_obs_output,
+          "add_id_to_obs": state.add_id_to_obs
+        ]
+        newState
+      },
+      toState: {id, output, state ->
+        def keysToRemove = ["add_id_to_obs", "add_id_obs_output", "add_id_make_observation_keys_unique"]
+        def newState = state.findAll{it.key !in keysToRemove}
+        newState + ["input": output.output]
+      }
+    )
+
+    | spatial_neighborhood_graph.run(
+      fromState: {id, state -> [
+        "input": state.input,
+        "modality": state.modality,
+        "layer": state.layer,
+        "input_obsm_spatial_coords": state.input_obsm_spatial_coords,
+        "coord_type": state.coord_type,
+        "n_spatial_neighbors": state.n_spatial_neighbors,
+        "delaunay": state.delaunay
+      ]},
+      toState: {id, output, state -> 
+          def keysToRemove = ["input_obsm_spatial_coords", "coord_type", "n_spatial_neighbors", "delaunay"]
+          def newState = state.findAll{it.key !in keysToRemove}
+          newState + ["input": output.output]
+        }
+    )
+
+    | joinStates { ids, states ->
+      def newId = "merged"
+      // gather keys with unique values across states that should be combined
+      def new_state_non_unique_values = [
+        input: states.collect{it.input},
+        input_id: ids,
+        _meta: [join_id: ids[0]]
+      ]
+      // gather keys from different states
+      def all_state_keys = states.inject([].toSet()){ current_keys, state ->
+          def new_keys = current_keys + state.keySet()
+          return new_keys
+      }.minus(["output", "id", "input", "_meta"])
+      // Create the new state from the keys, values should be the same across samples
+      def new_state = all_state_keys.inject([:]){ old_state, argument_name ->
+          argument_values = states.collect{it.get(argument_name)}.unique()
+          assert argument_values.size() == 1, "Arguments should be the same across samples. Argument name: $argument_name, \
+                                                argument value: $argument_values"
+          // take the unique value from the set (there is only one)
+          def argument_value
+          argument_values.each { argument_value = it }
+          def current_state = old_state + [(argument_name): argument_value]
+          return current_state
+      }
+      def data_state = new_state_non_unique_values + new_state
+      [ newId, data_state ]
+    }
+
+    | obsp_block_concatenation.run(
+      fromState: { id, state -> [
+        "input": state.input,
+        "modality": state.modality,
+        "input_id": state.input_id
+      ]},
+      toState: {id, output, state -> 
+          def keysToRemove = ["input_id"]
+          def newState = state.findAll{it.key !in keysToRemove}
+          newState + ["input": output.output]
+        }
+    )
+
+    | nichecompass.run(
+      fromState: {id, state -> [
+        "input": state.input,
+        "input_gp_mask": state.input_gp_mask,
+        "input_obs_covariates": state.input_obs_covariates,
+        "modality": state.modality,
+        "layer": state.layer,
+        "min_genes_per_gp": state.min_genes_per_gp,
+        "min_source_genes_per_gp": state.min_source_genes_per_gp,
+        "min_target_genes_per_gp": state.min_target_genes_per_gp,
+        "max_genes_per_gp": state.max_genes_per_gp,
+        "max_source_genes_per_gp": state.max_source_genes_per_gp,
+        "max_target_genes_per_gp": state.max_target_genes_per_gp,
+        "filter_genes_not_in_masks": state.filter_genes_not_in_masks,
+        "covariate_edges": state.covariate_edges,
+        "gene_expr_recon_distribution": state.gene_expr_recon_dist,
+        "log_variational": state.log_variational,
+        "node_label_method": state.node_label_method,
+        "active_gp_thresh_ratio": state.active_gp_thresh_ratio,
+        "active_gp_type": state.active_gp_type,
+        "n_addon_gp": state.n_addon_gp,
+        "cat_covariates_embeds_nums": state.cat_covariates_embeds_nums,
+        "random_state": state.random_state,
+        "n_epochs": state.n_epochs,
+        "n_epochs_all_gps": state.n_epochs_all_gps,
+        "n_epochs_no_edge_recon": state.n_epochs_no_edge_recon,
+        "n_epochs_no_cat_covariates_contrastive_loss": state.n_epochs_no_cat_covariates_contrastive_loss,
+        "lr": state.lr,
+        "weight_decay": state.weight_decay,
+        "edge_val_ratio": state.edge_val_ratio,
+        "node_val_ratio": state.node_val_ratio,
+        "edge_batch_size": state.edge_batch_size,
+        "node_batch_size": state.node_batch_size,
+        "n_sampled_neighbors": state.n_sampled_neighbors,
+        "output_obsm_embedding": state.output_obsm_embedding,
+        "output_model": state.output_model
+      ]},
+      args: [
+        "input_obsm_spatial_connectivities": "spatial_connectivities"
+      ],
+      toState: [
+        "input": "output",
+        "output_model": "output_model"
+      ]
+    )
+
+    | neighbors_leiden_umap.run(
+      fromState: { id, state -> [
+        "input": state.input,
+        "modality": state.modality,
+        "obsm_input": state.output_obsm_embedding,
+        "output": state.workflow_output,
+        "uns_neighbors": state.uns_neighbors,
+        "obsp_neighbor_distances": state.obsp_neighbor_distances,
+        "obsp_neighbor_connectivities": state.obsp_neighbor_connectivities,
+        "leiden_resolution": state.leiden_resolution,
+        "obs_cluster": state.obs_cluster,
+        "obsm_umap": state.obsm_umap,
+      ]},
+      toState: ["output": "output"]
+    )
+
+    | setState(["output": "output", "output_model": "output_model", "_meta": "_meta"])
+
+    | view()
+
+  emit:
+    output_ch
+}
--- a/src/workflows/niche/nichecompass_leiden/nextflow.config
+++ b/src/workflows/niche/nichecompass_leiden/nextflow.config
@@ -0,0 +1,10 @@
+manifest {
+  nextflowVersion = '!>=20.12.1-edge'
+}
+
+params {
+  rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString()
+}
+
+// include common settings
+includeConfig("${params.rootDir}/src/workflows/utils/labels.config")
--- a/src/workflows/niche/nichecompass_leiden/test.nf
+++ b/src/workflows/niche/nichecompass_leiden/test.nf
@@ -0,0 +1,70 @@
+nextflow.enable.dsl=2
+
+include { nichecompass_leiden } from params.rootDir + "/target/nextflow/workflows/niche/nichecompass_leiden/main.nf"
+include { nichecompass_leiden_test } from params.rootDir + "/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/main.nf"
+
+params.resources_test = params.rootDir + "/resources_test"
+
+workflow test_wf {
+
+  resources_test = file(params.resources_test)
+
+  output_ch = 
+    Channel.fromList([
+      [
+        id: "xenium",
+        input: resources_test.resolve("xenium/xenium_tiny.h5mu"),
+        input_gp_mask: resources_test.resolve("niche/prior_knowledge_gp_mask.json"),
+        n_epochs: 1,
+        n_epochs_all_gps: 0,
+        n_epochs_no_edge_recon: 0,
+        n_epochs_no_cat_covariates_contrastive_loss: 0,
+        output_model: "simple_execution_test_model"
+      ],
+      [
+        id: "cosmx",
+        input: resources_test.resolve("cosmx/Lung5_Rep2_tiny.h5mu"),
+        input_gp_mask: resources_test.resolve("niche/prior_knowledge_gp_mask.json"),
+        n_epochs: 1,
+        n_epochs_all_gps: 0,
+        n_epochs_no_edge_recon: 0,
+        n_epochs_no_cat_covariates_contrastive_loss: 0,
+        output_model: "simple_execution_test_model"
+      ]
+    ])
+    | map { state -> [state.id, state] }
+    | nichecompass_leiden.run(
+      toState: { id, output, state -> output + [og_input: state.input] }
+    )
+
+    | view { output ->
+      assert output.size() == 2 : "Outputs should contain two elements; [id, state]"
+
+      // check id
+      def id = output[0]
+      assert id == "merged"
+
+      // check output
+      def state = output[1]
+      assert state instanceof Map : "State should be a map. Found: ${state}"
+      assert state.containsKey("output") : "Output should contain key 'output'."
+      assert state.output.isFile() : "'output' should be a file."
+      assert state.output.toString().endsWith(".h5mu") : "Output file should end with '.h5mu'. Found: ${state.output}"
+      
+      // check model_output
+      assert state.containsKey("output_model") : "Output should contain key 'output_model'."
+      assert state.output_model.isDirectory() : "'output_model' should be a directory."
+      assert state.output_model.toString().endsWith("_model") : "Model output directory should end with '_model'. Found: ${state.output_model}"
+      
+      "Output: $output"
+    }
+    | nichecompass_leiden_test.run(
+      fromState: [
+        "input": "output"
+      ]
+    )
+    | toSortedList({a, b -> a[0] <=> b[0]})
+    | map { output_list ->
+      assert output_list.size() == 1 : "output channel should contain 1 events"
+    }
+}
--- a/src/workflows/test_workflows/niche/nichecompass_leiden/config.vsh.yaml
+++ b/src/workflows/test_workflows/niche/nichecompass_leiden/config.vsh.yaml
@@ -0,0 +1,25 @@
+name: "nichecompass_leiden_test"
+namespace: "test_workflows/niche"
+scope: "test"
+description: "This component tests the output of nichecompass leiden workflow."
+authors:
+  - __merge__: /src/authors/dorien_roosen.yaml
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: "--input"
+        type: file
+        required: true
+        description: Path to h5mu output.
+        example: foo.h5mu
+resources:
+  - type: python_script
+    path: script.py
+  - path: /src/utils/setup_logger.py
+engines:
+  - type: docker
+    image: python:3.12-slim
+    __merge__: /src/base/requirements/testworkflows_setup.yaml
+runners:
+  - type: executable
+  - type: nextflow
--- a/src/workflows/test_workflows/niche/nichecompass_leiden/script.py
+++ b/src/workflows/test_workflows/niche/nichecompass_leiden/script.py
@@ -0,0 +1,64 @@
+from mudata import read_h5mu
+import sys
+import pytest
+
+##VIASH START
+par = {"input": "nichecompass_leiden/output.h5mu"}
+
+meta = {"resources_dir": "resources_test"}
+##VIASH END
+
+
+def test_run():
+    input_mudata = read_h5mu(par["input"])
+
+    expected_mod = ["rna"]
+    expected_obsm = ["X_leiden_nichecompass_umap", "nichecompass_latent"]
+    expected_obs = ["sample_id", "nichecompass_leiden_1.0"]
+    expected_obsp = [
+        "spatial_distances",
+        "spatial_connectivities",
+        "nichecompass_connectivities",
+        "nichecompass_distances"
+    ]
+    expected_varm = [
+        "nichecompass_gp_sources",
+        "nichecompass_gp_targets",
+        "nichecompass_gp_sources_categories",
+        "nichecompass_gp_targets_categories"
+    ]
+    expected_uns = [
+        "nichecompass_sources_categories_label_encoder",
+        "nichecompass_targets_categories_label_encoder",
+        "nichecompass_source_genes_idx",
+        "nichecompass_target_genes_idx",
+        "nichecompass_genes_idx",
+        "nichecompass_gp_names",
+        "nichecompass_active_gp_names",
+        "nichecompass_neighbors",
+        "spatial",
+        "xenium_spatial_neighbors"
+    ]
+
+    assert all(key in list(input_mudata.mod) for key in expected_mod), (
+        f"Input modalities should be: {expected_mod}, found: {input_mudata.mod.keys()}."
+    )
+    assert all(key in list(input_mudata.mod["rna"].obsm) for key in expected_obsm), (
+        f"Input mod['rna'] obsm columns should be: {expected_obsm}, found: {input_mudata.mod['rna'].obsm.keys()}."
+    )
+    assert all(key in list(input_mudata.mod["rna"].obs) for key in expected_obs), (
+        f"Input mod['rna'] obs columns should be: {expected_obs}, found: {input_mudata.mod['rna'].obs.keys()}."
+    )
+    assert all(key in list(input_mudata.mod["rna"].obsp) for key in expected_obsp), (
+        f"Input mod['rna'] obsp columns should be: {expected_obsp}, found: {input_mudata.mod['rna'].obsp.keys()}."
+    )
+    assert all(key in list(input_mudata.mod["rna"].uns) for key in expected_uns), (
+        f"Input mod['rna'] uns columns should be: {expected_uns}, found: {input_mudata.mod['rna'].uns.keys()}."
+    )
+    assert all(key in list(input_mudata.mod["rna"].varm) for key in expected_varm), (
+        f"Input mod['rna'] varm columns should be: {expected_varm}, found: {input_mudata.mod['rna'].varm.keys()}."
+    )
+
+
+if __name__ == "__main__":
+    sys.exit(pytest.main([__file__, "--import-mode=importlib"]))
--- a/target/_private/executable/filter/subset_cosmx/.config.vsh.yaml
+++ b/target/_private/executable/filter/subset_cosmx/.config.vsh.yaml
@@ -228,7 +228,7 @@ build_info:
  output: "target/_private/executable/filter/subset_cosmx"
  executable: "target/_private/executable/filter/subset_cosmx/subset_cosmx"
  viash_version: "0.9.4"
-  git_commit: "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/_private/executable/filter/subset_cosmx/subset_cosmx
+++ b/target/_private/executable/filter/subset_cosmx/subset_cosmx
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component filter subset_cosmx"
-LABEL org.opencontainers.image.created="2025-12-08T20:39:05Z"
+LABEL org.opencontainers.image.created="2025-12-13T13:27:07Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+LABEL org.opencontainers.image.revision="9151204629228da14d7c82f49f24c607efb9251e"
 LABEL org.opencontainers.image.version="niche-compass"

 VIASHDOCKER
--- a/target/_private/nextflow/filter/subset_cosmx/.config.vsh.yaml
+++ b/target/_private/nextflow/filter/subset_cosmx/.config.vsh.yaml
@@ -228,7 +228,7 @@ build_info:
  output: "target/_private/nextflow/filter/subset_cosmx"
  executable: "target/_private/nextflow/filter/subset_cosmx/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/_private/nextflow/filter/subset_cosmx/main.nf
+++ b/target/_private/nextflow/filter/subset_cosmx/main.nf
@@ -3334,7 +3334,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/_private/nextflow/filter/subset_cosmx",
    "viash_version" : "0.9.4",
-    "git_commit" : "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831",
+    "git_commit" : "9151204629228da14d7c82f49f24c607efb9251e",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/_test/executable/test_workflows/niche/nichecompass_leiden_test/.config.vsh.yaml
+++ b/target/_test/executable/test_workflows/niche/nichecompass_leiden_test/.config.vsh.yaml
@@ -0,0 +1,185 @@
+name: "nichecompass_leiden_test"
+namespace: "test_workflows/niche"
+version: "niche-compass"
+authors:
+- name: "Dorien Roosen"
+  info:
+    role: "Core Team Member"
+    links:
+      email: "dorien@data-intuitive.com"
+      github: "dorien-er"
+      linkedin: "dorien-roosen"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "Path to h5mu output."
+    info: null
+    example:
+    - "foo.h5mu"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "python_script"
+  path: "script.py"
+  is_executable: true
+- type: "file"
+  path: "setup_logger.py"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
+description: "This component tests the output of nichecompass leiden workflow."
+info: null
+status: "enabled"
+scope:
+  image: "test"
+  target: "test"
+repositories:
+- type: "vsh"
+  name: "openpipeline"
+  repo: "openpipeline"
+  tag: "v3.0.0"
+links:
+  repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
+  docker_registry: "ghcr.io"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "python:3.12-slim"
+  target_registry: "images.viash-hub.com"
+  target_tag: "niche-compass"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "procps"
+    - "git"
+    interactive: false
+  - type: "python"
+    user: false
+    packages:
+    - "anndata~=0.11.1"
+    - "mudata~=0.3.1"
+    - "viashpy==0.9.0"
+    github:
+    - "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
+    script:
+    - "exec(\"try:\\n  import awkward\\nexcept ModuleNotFoundError:\\n  exit(0)\\\
+      nelse:  exit(1)\")"
+    upgrade: true
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/workflows/test_workflows/niche/nichecompass_leiden/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/_test/executable/test_workflows/niche/nichecompass_leiden_test"
+  executable: "target/_test/executable/test_workflows/niche/nichecompass_leiden_test/nichecompass_leiden_test"
+  viash_version: "0.9.4"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
+  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
+package_config:
+  name: "openpipeline_spatial"
+  version: "niche-compass"
+  info:
+    test_resources:
+    - type: "s3"
+      path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
+      dest: "resources_test"
+  repositories:
+  - type: "vsh"
+    name: "openpipeline"
+    repo: "openpipeline"
+    tag: "v3.0.0"
+  viash_version: "0.9.4"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
+    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    )'"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'niche-compass'"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
+    docker_registry: "ghcr.io"
--- a/target/_test/executable/test_workflows/niche/nichecompass_leiden_test/nextflow_labels.config
+++ b/target/_test/executable/test_workflows/niche/nichecompass_leiden_test/nextflow_labels.config
--- a/target/_test/executable/test_workflows/niche/nichecompass_leiden_test/nichecompass_leiden_test
+++ b/target/_test/executable/test_workflows/niche/nichecompass_leiden_test/nichecompass_leiden_test
--- a/target/_test/executable/test_workflows/niche/nichecompass_leiden_test/setup_logger.py
+++ b/target/_test/executable/test_workflows/niche/nichecompass_leiden_test/setup_logger.py
--- a/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/.config.vsh.yaml
+++ b/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/.config.vsh.yaml
@@ -0,0 +1,185 @@
+name: "nichecompass_leiden_test"
+namespace: "test_workflows/niche"
+version: "niche-compass"
+authors:
+- name: "Dorien Roosen"
+  info:
+    role: "Core Team Member"
+    links:
+      email: "dorien@data-intuitive.com"
+      github: "dorien-er"
+      linkedin: "dorien-roosen"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "Path to h5mu output."
+    info: null
+    example:
+    - "foo.h5mu"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "python_script"
+  path: "script.py"
+  is_executable: true
+- type: "file"
+  path: "setup_logger.py"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
+description: "This component tests the output of nichecompass leiden workflow."
+info: null
+status: "enabled"
+scope:
+  image: "test"
+  target: "test"
+repositories:
+- type: "vsh"
+  name: "openpipeline"
+  repo: "openpipeline"
+  tag: "v3.0.0"
+links:
+  repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
+  docker_registry: "ghcr.io"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "python:3.12-slim"
+  target_registry: "images.viash-hub.com"
+  target_tag: "niche-compass"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "procps"
+    - "git"
+    interactive: false
+  - type: "python"
+    user: false
+    packages:
+    - "anndata~=0.11.1"
+    - "mudata~=0.3.1"
+    - "viashpy==0.9.0"
+    github:
+    - "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
+    script:
+    - "exec(\"try:\\n  import awkward\\nexcept ModuleNotFoundError:\\n  exit(0)\\\
+      nelse:  exit(1)\")"
+    upgrade: true
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/workflows/test_workflows/niche/nichecompass_leiden/config.vsh.yaml"
+  runner: "nextflow"
+  engine: "docker|native"
+  output: "target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test"
+  executable: "target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/main.nf"
+  viash_version: "0.9.4"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
+  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
+package_config:
+  name: "openpipeline_spatial"
+  version: "niche-compass"
+  info:
+    test_resources:
+    - type: "s3"
+      path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
+      dest: "resources_test"
+  repositories:
+  - type: "vsh"
+    name: "openpipeline"
+    repo: "openpipeline"
+    tag: "v3.0.0"
+  viash_version: "0.9.4"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
+    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    )'"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'niche-compass'"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
+    docker_registry: "ghcr.io"
--- a/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/main.nf
+++ b/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/main.nf
--- a/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/nextflow.config
+++ b/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/nextflow.config
@@ -0,0 +1,126 @@
+manifest {
+  name = 'test_workflows/niche/nichecompass_leiden_test'
+  mainScript = 'main.nf'
+  nextflowVersion = '!>=20.12.1-edge'
+  version = 'niche-compass'
+  description = 'This component tests the output of nichecompass leiden workflow.'
+  author = 'Dorien Roosen'
+}
+
+process.container = 'nextflow/bash:latest'
+
+// detect tempdir
+tempDir = java.nio.file.Paths.get(
+  System.getenv('NXF_TEMP') ?:
+    System.getenv('VIASH_TEMP') ?: 
+    System.getenv('TEMPDIR') ?: 
+    System.getenv('TMPDIR') ?: 
+    '/tmp'
+).toAbsolutePath()
+
+profiles {
+  no_publish {
+    process {
+      withName: '.*' {
+        publishDir = [
+          enabled: false
+        ]
+      }
+    }
+  }
+  mount_temp {
+    docker.temp            = tempDir
+    podman.temp            = tempDir
+    charliecloud.temp      = tempDir
+  }
+  docker {
+    docker.enabled         = true
+    // docker.userEmulation   = true
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  singularity {
+    singularity.enabled    = true
+    singularity.autoMounts = true
+    docker.enabled         = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  podman {
+    podman.enabled         = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  shifter {
+    shifter.enabled        = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    charliecloud.enabled   = false
+  }
+  charliecloud {
+    charliecloud.enabled   = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+  }
+}
+
+process{
+  withLabel: mem1gb { memory = 1000000000.B }
+  withLabel: mem2gb { memory = 2000000000.B }
+  withLabel: mem5gb { memory = 5000000000.B }
+  withLabel: mem10gb { memory = 10000000000.B }
+  withLabel: mem20gb { memory = 20000000000.B }
+  withLabel: mem50gb { memory = 50000000000.B }
+  withLabel: mem100gb { memory = 100000000000.B }
+  withLabel: mem200gb { memory = 200000000000.B }
+  withLabel: mem500gb { memory = 500000000000.B }
+  withLabel: mem1tb { memory = 1000000000000.B }
+  withLabel: mem2tb { memory = 2000000000000.B }
+  withLabel: mem5tb { memory = 5000000000000.B }
+  withLabel: mem10tb { memory = 10000000000000.B }
+  withLabel: mem20tb { memory = 20000000000000.B }
+  withLabel: mem50tb { memory = 50000000000000.B }
+  withLabel: mem100tb { memory = 100000000000000.B }
+  withLabel: mem200tb { memory = 200000000000000.B }
+  withLabel: mem500tb { memory = 500000000000000.B }
+  withLabel: mem1gib { memory = 1073741824.B }
+  withLabel: mem2gib { memory = 2147483648.B }
+  withLabel: mem4gib { memory = 4294967296.B }
+  withLabel: mem8gib { memory = 8589934592.B }
+  withLabel: mem16gib { memory = 17179869184.B }
+  withLabel: mem32gib { memory = 34359738368.B }
+  withLabel: mem64gib { memory = 68719476736.B }
+  withLabel: mem128gib { memory = 137438953472.B }
+  withLabel: mem256gib { memory = 274877906944.B }
+  withLabel: mem512gib { memory = 549755813888.B }
+  withLabel: mem1tib { memory = 1099511627776.B }
+  withLabel: mem2tib { memory = 2199023255552.B }
+  withLabel: mem4tib { memory = 4398046511104.B }
+  withLabel: mem8tib { memory = 8796093022208.B }
+  withLabel: mem16tib { memory = 17592186044416.B }
+  withLabel: mem32tib { memory = 35184372088832.B }
+  withLabel: mem64tib { memory = 70368744177664.B }
+  withLabel: mem128tib { memory = 140737488355328.B }
+  withLabel: mem256tib { memory = 281474976710656.B }
+  withLabel: mem512tib { memory = 562949953421312.B }
+  withLabel: cpu1 { cpus = 1 }
+  withLabel: cpu2 { cpus = 2 }
+  withLabel: cpu5 { cpus = 5 }
+  withLabel: cpu10 { cpus = 10 }
+  withLabel: cpu20 { cpus = 20 }
+  withLabel: cpu50 { cpus = 50 }
+  withLabel: cpu100 { cpus = 100 }
+  withLabel: cpu200 { cpus = 200 }
+  withLabel: cpu500 { cpus = 500 }
+  withLabel: cpu1000 { cpus = 1000 }
+}
+
+includeConfig("nextflow_labels.config")
--- a/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/nextflow_labels.config
+++ b/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/nextflow_labels.config
--- a/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/setup_logger.py
+++ b/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/setup_logger.py
--- a/target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml
@@ -301,7 +301,7 @@ build_info:
  output: "target/executable/convert/from_cells2stats_to_h5mu"
  executable: "target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu"
  viash_version: "0.9.4"
-  git_commit: "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu
+++ b/target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu
@@ -459,9 +459,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_cells2stats_to_h5mu"
-LABEL org.opencontainers.image.created="2025-12-08T20:39:06Z"
+LABEL org.opencontainers.image.created="2025-12-13T13:27:08Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+LABEL org.opencontainers.image.revision="9151204629228da14d7c82f49f24c607efb9251e"
 LABEL org.opencontainers.image.version="niche-compass"

 VIASHDOCKER
--- a/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml
@@ -238,7 +238,7 @@ build_info:
  output: "target/executable/convert/from_cosmx_to_h5mu"
  executable: "target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu"
  viash_version: "0.9.4"
-  git_commit: "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu
+++ b/target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu
@@ -460,9 +460,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_cosmx_to_h5mu"
-LABEL org.opencontainers.image.created="2025-12-08T20:39:07Z"
+LABEL org.opencontainers.image.created="2025-12-13T13:27:09Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+LABEL org.opencontainers.image.revision="9151204629228da14d7c82f49f24c607efb9251e"
 LABEL org.opencontainers.image.version="niche-compass"

 VIASHDOCKER
--- a/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml
+++ b/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml
@@ -234,7 +234,7 @@ build_info:
  output: "target/executable/convert/from_cosmx_to_spatialexperiment"
  executable: "target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment"
  viash_version: "0.9.4"
-  git_commit: "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment
+++ b/target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment
@@ -457,9 +457,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("BiocManager", quietly

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_cosmx_to_spatialexperiment"
-LABEL org.opencontainers.image.created="2025-12-08T20:39:06Z"
+LABEL org.opencontainers.image.created="2025-12-13T13:27:08Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+LABEL org.opencontainers.image.revision="9151204629228da14d7c82f49f24c607efb9251e"
 LABEL org.opencontainers.image.version="niche-compass"

 VIASHDOCKER
--- a/target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml
+++ b/target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml
@@ -224,7 +224,7 @@ build_info:
  output: "target/executable/convert/from_h5mu_to_spatialexperiment"
  executable: "target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment"
  viash_version: "0.9.4"
-  git_commit: "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment
+++ b/target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment
@@ -458,9 +458,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_h5mu_to_spatialexperiment"
-LABEL org.opencontainers.image.created="2025-12-08T20:39:07Z"
+LABEL org.opencontainers.image.created="2025-12-13T13:27:09Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+LABEL org.opencontainers.image.revision="9151204629228da14d7c82f49f24c607efb9251e"
 LABEL org.opencontainers.image.version="niche-compass"

 VIASHDOCKER
--- a/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
@@ -221,7 +221,7 @@ build_info:
  output: "target/executable/convert/from_spatialdata_to_h5mu"
  executable: "target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu"
  viash_version: "0.9.4"
-  git_commit: "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu
+++ b/target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu
@@ -459,9 +459,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_spatialdata_to_h5mu"
-LABEL org.opencontainers.image.created="2025-12-08T20:39:06Z"
+LABEL org.opencontainers.image.created="2025-12-13T13:27:07Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+LABEL org.opencontainers.image.revision="9151204629228da14d7c82f49f24c607efb9251e"
 LABEL org.opencontainers.image.version="niche-compass"

 VIASHDOCKER
--- a/target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml
@@ -244,7 +244,7 @@ build_info:
  output: "target/executable/convert/from_xenium_to_h5mu"
  executable: "target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu"
  viash_version: "0.9.4"
-  git_commit: "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu
+++ b/target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu
@@ -459,9 +459,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_xenium_to_h5mu"
-LABEL org.opencontainers.image.created="2025-12-08T20:39:06Z"
+LABEL org.opencontainers.image.created="2025-12-13T13:27:08Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+LABEL org.opencontainers.image.revision="9151204629228da14d7c82f49f24c607efb9251e"
 LABEL org.opencontainers.image.version="niche-compass"

 VIASHDOCKER
--- a/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml
+++ b/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml
@@ -326,7 +326,7 @@ build_info:
  output: "target/executable/convert/from_xenium_to_spatialdata"
  executable: "target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata"
  viash_version: "0.9.4"
-  git_commit: "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata
+++ b/target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata
@@ -459,9 +459,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_xenium_to_spatialdata"
-LABEL org.opencontainers.image.created="2025-12-08T20:39:05Z"
+LABEL org.opencontainers.image.created="2025-12-13T13:27:09Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+LABEL org.opencontainers.image.revision="9151204629228da14d7c82f49f24c607efb9251e"
 LABEL org.opencontainers.image.version="niche-compass"

 VIASHDOCKER
--- a/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml
+++ b/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml
@@ -224,7 +224,7 @@ build_info:
  output: "target/executable/convert/from_xenium_to_spatialexperiment"
  executable: "target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment"
  viash_version: "0.9.4"
-  git_commit: "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment
+++ b/target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment
@@ -457,9 +457,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("BiocManager", quietly

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_xenium_to_spatialexperiment"
-LABEL org.opencontainers.image.created="2025-12-08T20:39:06Z"
+LABEL org.opencontainers.image.created="2025-12-13T13:27:08Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+LABEL org.opencontainers.image.revision="9151204629228da14d7c82f49f24c607efb9251e"
 LABEL org.opencontainers.image.version="niche-compass"

 VIASHDOCKER
--- a/target/executable/dataflow/obsp_block_concatenation/.config.vsh.yaml
+++ b/target/executable/dataflow/obsp_block_concatenation/.config.vsh.yaml
@@ -296,7 +296,7 @@ build_info:
  output: "target/executable/dataflow/obsp_block_concatenation"
  executable: "target/executable/dataflow/obsp_block_concatenation/obsp_block_concatenation"
  viash_version: "0.9.4"
-  git_commit: "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/executable/dataflow/obsp_block_concatenation/obsp_block_concatenation
+++ b/target/executable/dataflow/obsp_block_concatenation/obsp_block_concatenation
@@ -459,9 +459,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dries Schaumont, Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component dataflow obsp_block_concatenation"
-LABEL org.opencontainers.image.created="2025-12-08T20:39:07Z"
+LABEL org.opencontainers.image.created="2025-12-13T13:27:09Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+LABEL org.opencontainers.image.revision="9151204629228da14d7c82f49f24c607efb9251e"
 LABEL org.opencontainers.image.version="niche-compass"

 VIASHDOCKER
--- a/target/executable/mapping/spaceranger_count/.config.vsh.yaml
+++ b/target/executable/mapping/spaceranger_count/.config.vsh.yaml
@@ -426,7 +426,7 @@ build_info:
  output: "target/executable/mapping/spaceranger_count"
  executable: "target/executable/mapping/spaceranger_count/spaceranger_count"
  viash_version: "0.9.4"
-  git_commit: "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/executable/mapping/spaceranger_count/spaceranger_count
+++ b/target/executable/mapping/spaceranger_count/spaceranger_count
@@ -453,9 +453,9 @@ apt upgrade -y && apt install -y procps && rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.authors="Jakub Majercik"
 LABEL org.opencontainers.image.description="Companion container for running component mapping spaceranger_count"
-LABEL org.opencontainers.image.created="2025-12-08T20:39:07Z"
+LABEL org.opencontainers.image.created="2025-12-13T13:27:09Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+LABEL org.opencontainers.image.revision="9151204629228da14d7c82f49f24c607efb9251e"
 LABEL org.opencontainers.image.version="niche-compass"

 VIASHDOCKER
--- a/target/executable/neighbors/spatial_neighborhood_graph/.config.vsh.yaml
+++ b/target/executable/neighbors/spatial_neighborhood_graph/.config.vsh.yaml
@@ -1,5 +1,5 @@
-name: "neighbors"
-namespace: "spatial_neighborhood_graph"
+name: "spatial_neighborhood_graph"
+namespace: "neighbors"
 version: "niche-compass"
 authors:
 - name: "Dorien Roosen"
@@ -269,10 +269,10 @@ build_info:
  config: "src/neighbors/spatial_neighborhood_graph/config.vsh.yaml"
  runner: "executable"
  engine: "docker|native"
-  output: "target/executable/spatial_neighborhood_graph/neighbors"
-  executable: "target/executable/spatial_neighborhood_graph/neighbors/neighbors"
+  output: "target/executable/neighbors/spatial_neighborhood_graph"
+  executable: "target/executable/neighbors/spatial_neighborhood_graph/spatial_neighborhood_graph"
  viash_version: "0.9.4"
-  git_commit: "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/executable/neighbors/spatial_neighborhood_graph/nextflow_labels.config
+++ b/target/executable/neighbors/spatial_neighborhood_graph/nextflow_labels.config
@@ -0,0 +1,68 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // CPU resources
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 4 }
+  withLabel: midcpu { cpus = 10 }
+  withLabel: highcpu { cpus = 20 }
+  
+  // Memory resources
+  withLabel: lowmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
+
+  // Disk space
+  // Nextflow apparently can't handle empty directives, i.e.
+  // withLabel: lowdisk {}
+  // so for that reason we have to add a dummy directive
+  withLabel: lowdisk {
+    dummyDirective = "dummyValue"
+  }
+  withLabel: middisk {
+    dummyDirective = "dummyValue"
+  }
+  withLabel: highdisk {
+    dummyDirective = "dummyValue"
+  }
+  withLabel: veryhighdisk {
+    dummyDirective = "dummyValue"
+  }
+  // NOTE: The above labels intentionally do not have an effect by default.
+  // The user should set the disk space requirements by adding the following
+  // to the compute environment:
+  //
+  // withLabel: lowdisk { disk = { 20.GB * task.attempt } }
+  // withLabel: middisk { disk = { 100.GB * task.attempt } }
+  // withLabel: highdisk { disk = { 200.GB * task.attempt } }
+  // withLabel: veryhighdisk { disk = { 500.GB * task.attempt } }
+}
+
+def get_memory(to_compare) {
+  if (!process.containsKey("maxMemory") || !process.maxMemory) {
+    return to_compare
+  }
+
+  try {
+    if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
+      return process.maxMemory
+    }
+    else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
+      return max_memory as nextflow.util.MemoryUnit
+    }
+    else {
+      return to_compare
+    }  
+  } catch (all) {
+        println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
+        System.exit(1)
+  }
+}
--- a/target/executable/neighbors/spatial_neighborhood_graph/setup_logger.py
+++ b/target/executable/neighbors/spatial_neighborhood_graph/setup_logger.py
@@ -0,0 +1,12 @@
+def setup_logger():
+    import logging
+    from sys import stdout
+
+    logger = logging.getLogger()
+    logger.setLevel(logging.INFO)
+    console_handler = logging.StreamHandler(stdout)
+    logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
+    console_handler.setFormatter(logFormatter)
+    logger.addHandler(console_handler)
+
+    return logger
--- a/target/executable/neighbors/spatial_neighborhood_graph/spatial_neighborhood_graph
+++ b/target/executable/neighbors/spatial_neighborhood_graph/spatial_neighborhood_graph
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# neighbors niche-compass
+# spatial_neighborhood_graph niche-compass
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -165,8 +165,8 @@ VIASH_META_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}`
 VIASH_TARGET_DIR=`ViashFindTargetDir $VIASH_META_RESOURCES_DIR`

 # define meta fields
-VIASH_META_NAME="neighbors"
-VIASH_META_FUNCTIONALITY_NAME="neighbors"
+VIASH_META_NAME="spatial_neighborhood_graph"
+VIASH_META_FUNCTIONALITY_NAME="spatial_neighborhood_graph"
 VIASH_META_EXECUTABLE="$VIASH_META_RESOURCES_DIR/$VIASH_META_NAME"
 VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
 VIASH_META_TEMP_DIR="$VIASH_TEMP"
@@ -457,10 +457,10 @@ RUN pip install --upgrade pip && \
  python -c 'exec("try:\n  import awkward\nexcept ModuleNotFoundError:\n  exit(0)\nelse:  exit(1)")'

 LABEL org.opencontainers.image.authors="Dorien Roosen"
-LABEL org.opencontainers.image.description="Companion container for running component spatial_neighborhood_graph neighbors"
-LABEL org.opencontainers.image.created="2025-12-08T20:39:06Z"
+LABEL org.opencontainers.image.description="Companion container for running component neighbors spatial_neighborhood_graph"
+LABEL org.opencontainers.image.created="2025-12-13T13:27:08Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+LABEL org.opencontainers.image.revision="9151204629228da14d7c82f49f24c607efb9251e"
 LABEL org.opencontainers.image.version="niche-compass"

 VIASHDOCKER
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "neighbors niche-compass"
+  echo "spatial_neighborhood_graph niche-compass"
  echo ""
  echo "Calculates a spatial neighborhood graph."
  echo ""
@@ -687,7 +687,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "neighbors niche-compass"
+            echo "spatial_neighborhood_graph niche-compass"
            exit
            ;;
        --input)
@@ -877,7 +877,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/spatial_neighborhood_graph/neighbors:niche-compass'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/neighbors/spatial_neighborhood_graph:niche-compass'
  fi

  # print dockerfile
@@ -1207,7 +1207,7 @@ fi
 ViashDebug "Running command: $(echo $VIASH_CMD)"
 cat << VIASHEOF | eval $VIASH_CMD
 set -e
-tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-neighbors-XXXXXX").py
+tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-spatial_neighborhood_graph-XXXXXX").py
 function clean_up {
  rm "\$tempscript"
 }
--- a/target/executable/nichecompass/gene_program_mask/.config.vsh.yaml
+++ b/target/executable/nichecompass/gene_program_mask/.config.vsh.yaml
@@ -0,0 +1,469 @@
+name: "gene_program_mask"
+namespace: "nichecompass"
+version: "niche-compass"
+authors:
+- name: "Dorien Roosen"
+  roles:
+  - "maintainer"
+  info:
+    role: "Core Team Member"
+    links:
+      email: "dorien@data-intuitive.com"
+      github: "dorien-er"
+      linkedin: "dorien-roosen"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--input_gene_orthologs_mapping_file"
+    description: "Path to a CSV file mapping human genes to mouse orthologs.\nRequired\
+      \ for the OmniPath and NicheNet masks if `--species mouse`.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--input_metabolite_enzymes"
+    description: "Path to the MeBocost metabolite-enzymes TSV file.\nRequired for\
+      \ generating the MeBocost gene program mask.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--input_metabolite_sensors"
+    description: "Path to the MeBocost metabolite-sensors TSV file.\nRequired for\
+      \ generating the MeBocost gene program mask.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Parameters"
+  arguments:
+  - type: "string"
+    name: "--species"
+    description: "Species of the organism (human or mouse)."
+    info: null
+    default:
+    - "human"
+    required: false
+    choices:
+    - "human"
+    - "mouse"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--create_omnipath_gene_program_mask"
+    description: "Whether to create the OmniPath gene program mask."
+    info: null
+    default:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--create_nichenet_gene_program_mask"
+    description: "Whether to create the NicheNet gene program mask."
+    info: null
+    default:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--create_mebocost_gene_program_mask"
+    description: "Whether to create the MeBocost gene program mask."
+    info: null
+    default:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--create_collectri_tf_gene_program_mask"
+    description: "Whether to create the CollecTRI TF gene program mask."
+    info: null
+    default:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--overlap_thresh_target_genes"
+    description: "The minimum ratio of target genes that need to overlap between a\
+      \ GP without source genes and another GP for the GP to be dropped.\nGene programs\
+      \ with different source genes are never combined or dropped.\n"
+    info: null
+    default:
+    - 1.0
+    required: false
+    min: 0.0
+    max: 1.0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Omnipath Parameters"
+  arguments:
+  - type: "integer"
+    name: "--omnipath_min_curation_effort"
+    description: "Minimum number of times an interaction has to be described in a\
+      \ paper and mentioned in a database to be included in the OmniPath gene programs."
+    info: null
+    default:
+    - 2
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "NicheNet Parameters"
+  arguments:
+  - type: "string"
+    name: "--nichenet_version"
+    description: "Version of the NicheNet ligand receptor network and ligand target\
+      \ gene regulatory potential matrix.\n´v2´ is an improved version of ´v1´, and\
+      \ has separate files for mouse and human.\n"
+    info: null
+    default:
+    - "v2"
+    required: false
+    choices:
+    - "v1"
+    - "v2"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--nichenet_keep_target_genes_ratio"
+    description: "Ratio of target genes that are kept compared to total target genes.\n\
+      This ratio is applied over the entire matrix (not on gene program level), and\
+      \ determines the ´all_gps_score_keep_threshold´, which will be used to filter\
+      \ target genes according to their regulatory potential scores.\n"
+    info: null
+    default:
+    - 1.0
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--nichenet_max_n_target_genes_per_gp"
+    description: "Maximum number of target genes per gene program. If a gene program\
+      \ has more target genes than ´max_n_target_genes_per_gp´, only the ´max_n_target_genes_per_gp´\
+      \ gene programs with the highest regulatory potential scores will be kept.\n\
+      Default value is chosen based on MultiNicheNet specification (s. Browaeys, R.\
+      \ et al. MultiNicheNet: a flexible framework for differential cell-cell communication\
+      \ analysis from multi-sample multi-condition single-cell transcriptomics data.\
+      \ bioRxiv (2023) doi:10.1101/2023.06.13.544751).\n"
+    info: null
+    default:
+    - 250
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "Path to the output gene program mask JSON file."
+    info: null
+    example:
+    - "gp_mask.json"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_omnipath_lr_network"
+    description: "Path to the output OmniPath ligand-receptor network CSV file."
+    info: null
+    example:
+    - "omnipath_lr_network.csv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_nichenet_lr_network"
+    description: "Path to the output NicheNet ligand-receptor network CSV file."
+    info: null
+    example:
+    - "nichenet_lr_network.csv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_nichenet_ligand_target_matrix"
+    description: "Path to the output NicheNet ligand-target gene regulatory potential\
+      \ matrix file."
+    info: null
+    example:
+    - "nichenet_ligand_target_matrix.csv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_collectri_tf_network"
+    description: "Path to the output CollecTRI TF-target gene regulatory potential\
+      \ network CSV file."
+    info: null
+    example:
+    - "collectri_tf_network.csv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_omnipath_gp_gene_count_distributions"
+    description: "Path to save the OmniPath gene program gene count distributions\
+      \ plot."
+    info: null
+    example:
+    - "omnipath_gp_gene_count_distributions.svg"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_nichenet_gp_gene_count_distributions"
+    description: "Path to save the NicheNet gene program gene count distributions\
+      \ plot."
+    info: null
+    example:
+    - "nichenet_gp_gene_count_distributions.svg"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_mebocost_gp_gene_count_distributions"
+    description: "Path to save the MeBocost gene program gene count distributions\
+      \ plot."
+    info: null
+    example:
+    - "mebocost_gp_gene_count_distributions.svg"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_collectri_tf_gp_gene_count_distributions"
+    description: "Path to save the CollecTRI TF gene program gene count distributions\
+      \ plot."
+    info: null
+    example:
+    - "collectri_tf_gp_gene_count_distributions.svg"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "python_script"
+  path: "script.py"
+  is_executable: true
+- type: "file"
+  path: "setup_logger.py"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
+description: "Generation of a prior knowledge gene program mask for NicheCompass."
+test_resources:
+- type: "python_script"
+  path: "test.py"
+  is_executable: true
+- type: "file"
+  path: "niche"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+repositories:
+- type: "vsh"
+  name: "openpipeline"
+  repo: "openpipeline"
+  tag: "v3.0.0"
+links:
+  repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
+  docker_registry: "ghcr.io"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    label:
+    - "lowcpu"
+    - "lowmem"
+    - "lowdisk"
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "nvidia/cuda:12.4.1-cudnn-devel-ubuntu22.04"
+  target_registry: "images.viash-hub.com"
+  target_tag: "niche-compass"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "libhdf5-dev"
+    - "python3-pip"
+    - "python3-dev"
+    - "python-is-python3"
+    interactive: false
+  - type: "docker"
+    run:
+    - "pip install torch --index-url https://download.pytorch.org/whl/cu124 \\\n&&\
+      \ pip install pyg_lib torch-scatter torch-sparse -f https://data.pyg.org/whl/torch-2.6.0+cu124.html\
+      \   \n"
+  - type: "python"
+    user: false
+    packages:
+    - "numpy<2"
+    - "nichecompass"
+    upgrade: true
+  test_setup:
+  - type: "python"
+    user: false
+    packages:
+    - "viashpy==0.9.0"
+    upgrade: true
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/nichecompass/gene_program_mask/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/nichecompass/gene_program_mask"
+  executable: "target/executable/nichecompass/gene_program_mask/gene_program_mask"
+  viash_version: "0.9.4"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
+  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
+package_config:
+  name: "openpipeline_spatial"
+  version: "niche-compass"
+  info:
+    test_resources:
+    - type: "s3"
+      path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
+      dest: "resources_test"
+  repositories:
+  - type: "vsh"
+    name: "openpipeline"
+    repo: "openpipeline"
+    tag: "v3.0.0"
+  viash_version: "0.9.4"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
+    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    )'"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'niche-compass'"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
+    docker_registry: "ghcr.io"
--- a/target/executable/nichecompass/gene_program_mask/gene_program_mask
+++ b/target/executable/nichecompass/gene_program_mask/gene_program_mask
--- a/target/executable/nichecompass/gene_program_mask/nextflow_labels.config
+++ b/target/executable/nichecompass/gene_program_mask/nextflow_labels.config
@@ -0,0 +1,68 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // CPU resources
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 4 }
+  withLabel: midcpu { cpus = 10 }
+  withLabel: highcpu { cpus = 20 }
+  
+  // Memory resources
+  withLabel: lowmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
+
+  // Disk space
+  // Nextflow apparently can't handle empty directives, i.e.
+  // withLabel: lowdisk {}
+  // so for that reason we have to add a dummy directive
+  withLabel: lowdisk {
+    dummyDirective = "dummyValue"
+  }
+  withLabel: middisk {
+    dummyDirective = "dummyValue"
+  }
+  withLabel: highdisk {
+    dummyDirective = "dummyValue"
+  }
+  withLabel: veryhighdisk {
+    dummyDirective = "dummyValue"
+  }
+  // NOTE: The above labels intentionally do not have an effect by default.
+  // The user should set the disk space requirements by adding the following
+  // to the compute environment:
+  //
+  // withLabel: lowdisk { disk = { 20.GB * task.attempt } }
+  // withLabel: middisk { disk = { 100.GB * task.attempt } }
+  // withLabel: highdisk { disk = { 200.GB * task.attempt } }
+  // withLabel: veryhighdisk { disk = { 500.GB * task.attempt } }
+}
+
+def get_memory(to_compare) {
+  if (!process.containsKey("maxMemory") || !process.maxMemory) {
+    return to_compare
+  }
+
+  try {
+    if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
+      return process.maxMemory
+    }
+    else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
+      return max_memory as nextflow.util.MemoryUnit
+    }
+    else {
+      return to_compare
+    }  
+  } catch (all) {
+        println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
+        System.exit(1)
+  }
+}
--- a/target/executable/nichecompass/gene_program_mask/setup_logger.py
+++ b/target/executable/nichecompass/gene_program_mask/setup_logger.py
@@ -0,0 +1,12 @@
+def setup_logger():
+    import logging
+    from sys import stdout
+
+    logger = logging.getLogger()
+    logger.setLevel(logging.INFO)
+    console_handler = logging.StreamHandler(stdout)
+    logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
+    console_handler.setFormatter(logFormatter)
+    logger.addHandler(console_handler)
+
+    return logger
--- a/target/executable/nichecompass/nichecompass/.config.vsh.yaml
+++ b/target/executable/nichecompass/nichecompass/.config.vsh.yaml
@@ -83,45 +83,6 @@ argument_groups:
    direction: "input"
    multiple: true
    multiple_sep: ";"
- name: "Spatial Neighbors Calculation"
-  arguments:
-  - type: "string"
-    name: "--coord_type"
-    description: "Type of coordinate system. Valid options are:\n`grid` - grid coordinates.\n\
-      `generic` - generic coordinates.\nIf not provided, `grid` is used if `--input_obsm_spatial_coords`\
-      \ is in --input .uns with `--n_neighs` = 6 (Visium), otherwise `generic` is\
-      \ used.\n"
-    info: null
-    required: false
-    choices:
-    - "generic"
-    - "grid"
-    direction: "input"
-    multiple: false
-    multiple_sep: ";"
-  - type: "integer"
-    name: "--n_spatial_neighbors"
-    description: "Depending on `--coord_type`:\n`grid` - number of neighboring tiles.\n\
-      `generic` - number of neighborhoods for non-grid data. Only used when `--delaunay\
-      \ False`.\n"
-    info: null
-    default:
-    - 6
-    required: false
-    direction: "input"
-    multiple: false
-    multiple_sep: ";"
-  - type: "boolean"
-    name: "--delaunay"
-    description: "Whether to use Delaunay triangulation to determine spatial neighborhood\
-      \ graph.\nOnly used when `--coord_type generic`.\n"
-    info: null
-    default:
-    - false
-    required: false
-    direction: "input"
-    multiple: false
-    multiple_sep: ";"
 - name: "Gene Program Mask"
  arguments:
  - type: "integer"
@@ -807,12 +768,12 @@ argument_groups:
    multiple: false
    multiple_sep: ";"
  - type: "string"
-    name: "--output_uns_gene_index"
+    name: "--output_uns_genes_index"
    description: "Key of the uns field where the index of a concatenated vector of\
      \ target and source genes that are in the gene program masks will be stored.\n"
    info: null
    default:
-    - "nichecompass_gene_idx"
+    - "nichecompass_genes_idx"
    required: false
    direction: "input"
    multiple: false
@@ -870,6 +831,20 @@ argument_groups:
    direction: "input"
    multiple: false
    multiple_sep: ";"
+  - type: "string"
+    name: "--output_compression"
+    description: "Compression format to use for the output AnnData and/or Mudata objects.\n\
+      By default no compression is applied.\n"
+    info: null
+    example:
+    - "gzip"
+    required: false
+    choices:
+    - "gzip"
+    - "lzf"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
 resources:
 - type: "python_script"
  path: "script.py"
@@ -1028,7 +1003,7 @@ build_info:
  output: "target/executable/nichecompass/nichecompass"
  executable: "target/executable/nichecompass/nichecompass/nichecompass"
  viash_version: "0.9.4"
-  git_commit: "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/executable/nichecompass/nichecompass/nichecompass
+++ b/target/executable/nichecompass/nichecompass/nichecompass
@@ -464,9 +464,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component nichecompass nichecompass"
-LABEL org.opencontainers.image.created="2025-12-08T20:39:06Z"
+LABEL org.opencontainers.image.created="2025-12-13T13:27:09Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+LABEL org.opencontainers.image.revision="9151204629228da14d7c82f49f24c607efb9251e"
 LABEL org.opencontainers.image.version="niche-compass"

 VIASHDOCKER
@@ -626,32 +626,6 @@ function ViashHelp {
  echo "        type: string, multiple values allowed"
  echo "        Keys of the adata.obs fields to use as covariates."
  echo ""
-  echo "Spatial Neighbors Calculation:"
-  echo "    --coord_type"
-  echo "        type: string"
-  echo "        choices: [ generic, grid ]"
-  echo "        Type of coordinate system. Valid options are:"
-  echo "        \`grid\` - grid coordinates."
-  echo "        \`generic\` - generic coordinates."
-  echo "        If not provided, \`grid\` is used if \`--input_obsm_spatial_coords\` is in"
-  echo "        --input .uns with \`--n_neighs\` = 6 (Visium), otherwise \`generic\` is"
-  echo "        used."
-  echo ""
-  echo "    --n_spatial_neighbors"
-  echo "        type: integer"
-  echo "        default: 6"
-  echo "        Depending on \`--coord_type\`:"
-  echo "        \`grid\` - number of neighboring tiles."
-  echo "        \`generic\` - number of neighborhoods for non-grid data. Only used when"
-  echo "        \`--delaunay False\`."
-  echo ""
-  echo "    --delaunay"
-  echo "        type: boolean"
-  echo "        default: false"
-  echo "        Whether to use Delaunay triangulation to determine spatial neighborhood"
-  echo "        graph."
-  echo "        Only used when \`--coord_type generic\`."
-  echo ""
  echo "Gene Program Mask:"
  echo "    --min_genes_per_gp"
  echo "        type: integer"
@@ -1063,9 +1037,9 @@ function ViashHelp {
  echo "        default: nichecompass_active_gp_names"
  echo "        Key of the uns field where the active gene program names will be stored."
  echo ""
-  echo "    --output_uns_gene_index"
+  echo "    --output_uns_genes_index"
  echo "        type: string"
-  echo "        default: nichecompass_gene_idx"
+  echo "        default: nichecompass_genes_idx"
  echo "        Key of the uns field where the index of a concatenated vector of target"
  echo "        and source genes that are in the gene program masks will be stored."
  echo ""
@@ -1098,6 +1072,13 @@ function ViashHelp {
  echo "        Key of the obsp field where the aggregation weights of the node label"
  echo "        aggregator will be stored."
  echo ""
+  echo "    --output_compression"
+  echo "        type: string"
+  echo "        example: gzip"
+  echo "        choices: [ gzip, lzf ]"
+  echo "        Compression format to use for the output AnnData and/or Mudata objects."
+  echo "        By default no compression is applied."
+  echo ""
  echo "Viash built in Computational Requirements:"
  echo "    ---cpus=INT"
  echo "        Number of CPUs to use"
@@ -1220,39 +1201,6 @@ while [[ $# -gt 0 ]]; do
            fi
            shift 1
            ;;
-        --coord_type)
-            [ -n "$VIASH_PAR_COORD_TYPE" ] && ViashError Bad arguments for option \'--coord_type\': \'$VIASH_PAR_COORD_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
-            VIASH_PAR_COORD_TYPE="$2"
-            [ $# -lt 2 ] && ViashError Not enough arguments passed to --coord_type. Use "--help" to get more information on the parameters. && exit 1
-            shift 2
-            ;;
-        --coord_type=*)
-            [ -n "$VIASH_PAR_COORD_TYPE" ] && ViashError Bad arguments for option \'--coord_type=*\': \'$VIASH_PAR_COORD_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
-            VIASH_PAR_COORD_TYPE=$(ViashRemoveFlags "$1")
-            shift 1
-            ;;
-        --n_spatial_neighbors)
-            [ -n "$VIASH_PAR_N_SPATIAL_NEIGHBORS" ] && ViashError Bad arguments for option \'--n_spatial_neighbors\': \'$VIASH_PAR_N_SPATIAL_NEIGHBORS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
-            VIASH_PAR_N_SPATIAL_NEIGHBORS="$2"
-            [ $# -lt 2 ] && ViashError Not enough arguments passed to --n_spatial_neighbors. Use "--help" to get more information on the parameters. && exit 1
-            shift 2
-            ;;
-        --n_spatial_neighbors=*)
-            [ -n "$VIASH_PAR_N_SPATIAL_NEIGHBORS" ] && ViashError Bad arguments for option \'--n_spatial_neighbors=*\': \'$VIASH_PAR_N_SPATIAL_NEIGHBORS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
-            VIASH_PAR_N_SPATIAL_NEIGHBORS=$(ViashRemoveFlags "$1")
-            shift 1
-            ;;
-        --delaunay)
-            [ -n "$VIASH_PAR_DELAUNAY" ] && ViashError Bad arguments for option \'--delaunay\': \'$VIASH_PAR_DELAUNAY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
-            VIASH_PAR_DELAUNAY="$2"
-            [ $# -lt 2 ] && ViashError Not enough arguments passed to --delaunay. Use "--help" to get more information on the parameters. && exit 1
-            shift 2
-            ;;
-        --delaunay=*)
-            [ -n "$VIASH_PAR_DELAUNAY" ] && ViashError Bad arguments for option \'--delaunay=*\': \'$VIASH_PAR_DELAUNAY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
-            VIASH_PAR_DELAUNAY=$(ViashRemoveFlags "$1")
-            shift 1
-            ;;
        --min_genes_per_gp)
            [ -n "$VIASH_PAR_MIN_GENES_PER_GP" ] && ViashError Bad arguments for option \'--min_genes_per_gp\': \'$VIASH_PAR_MIN_GENES_PER_GP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MIN_GENES_PER_GP="$2"
@@ -1893,15 +1841,15 @@ while [[ $# -gt 0 ]]; do
            VIASH_PAR_OUTPUT_UNS_ACTIVE_GP_NAMES=$(ViashRemoveFlags "$1")
            shift 1
            ;;
-        --output_uns_gene_index)
-            [ -n "$VIASH_PAR_OUTPUT_UNS_GENE_INDEX" ] && ViashError Bad arguments for option \'--output_uns_gene_index\': \'$VIASH_PAR_OUTPUT_UNS_GENE_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
-            VIASH_PAR_OUTPUT_UNS_GENE_INDEX="$2"
-            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_uns_gene_index. Use "--help" to get more information on the parameters. && exit 1
+        --output_uns_genes_index)
+            [ -n "$VIASH_PAR_OUTPUT_UNS_GENES_INDEX" ] && ViashError Bad arguments for option \'--output_uns_genes_index\': \'$VIASH_PAR_OUTPUT_UNS_GENES_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_OUTPUT_UNS_GENES_INDEX="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_uns_genes_index. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
-        --output_uns_gene_index=*)
-            [ -n "$VIASH_PAR_OUTPUT_UNS_GENE_INDEX" ] && ViashError Bad arguments for option \'--output_uns_gene_index=*\': \'$VIASH_PAR_OUTPUT_UNS_GENE_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
-            VIASH_PAR_OUTPUT_UNS_GENE_INDEX=$(ViashRemoveFlags "$1")
+        --output_uns_genes_index=*)
+            [ -n "$VIASH_PAR_OUTPUT_UNS_GENES_INDEX" ] && ViashError Bad arguments for option \'--output_uns_genes_index=*\': \'$VIASH_PAR_OUTPUT_UNS_GENES_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_OUTPUT_UNS_GENES_INDEX=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --output_uns_target_genes_index)
@@ -1965,6 +1913,17 @@ while [[ $# -gt 0 ]]; do
            VIASH_PAR_OUTPUT_OBSP_AGG_WEIGHTS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
+        --output_compression)
+            [ -n "$VIASH_PAR_OUTPUT_COMPRESSION" ] && ViashError Bad arguments for option \'--output_compression\': \'$VIASH_PAR_OUTPUT_COMPRESSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_OUTPUT_COMPRESSION="$2"
+            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_compression. Use "--help" to get more information on the parameters. && exit 1
+            shift 2
+            ;;
+        --output_compression=*)
+            [ -n "$VIASH_PAR_OUTPUT_COMPRESSION" ] && ViashError Bad arguments for option \'--output_compression=*\': \'$VIASH_PAR_OUTPUT_COMPRESSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_OUTPUT_COMPRESSION=$(ViashRemoveFlags "$1")
+            shift 1
+            ;;
        ---engine)
            VIASH_ENGINE_ID="$2"
            shift 2
@@ -2185,12 +2144,6 @@ fi
 if [ -z ${VIASH_PAR_INPUT_OBSM_SPATIAL_CONNECTIVITIES+x} ]; then
  VIASH_PAR_INPUT_OBSM_SPATIAL_CONNECTIVITIES="spatial_connectivities"
 fi
-if [ -z ${VIASH_PAR_N_SPATIAL_NEIGHBORS+x} ]; then
-  VIASH_PAR_N_SPATIAL_NEIGHBORS="6"
-fi
-if [ -z ${VIASH_PAR_DELAUNAY+x} ]; then
-  VIASH_PAR_DELAUNAY="false"
-fi
 if [ -z ${VIASH_PAR_MIN_GENES_PER_GP+x} ]; then
  VIASH_PAR_MIN_GENES_PER_GP="1"
 fi
@@ -2326,8 +2279,8 @@ fi
 if [ -z ${VIASH_PAR_OUTPUT_UNS_ACTIVE_GP_NAMES+x} ]; then
  VIASH_PAR_OUTPUT_UNS_ACTIVE_GP_NAMES="nichecompass_active_gp_names"
 fi
-if [ -z ${VIASH_PAR_OUTPUT_UNS_GENE_INDEX+x} ]; then
-  VIASH_PAR_OUTPUT_UNS_GENE_INDEX="nichecompass_gene_idx"
+if [ -z ${VIASH_PAR_OUTPUT_UNS_GENES_INDEX+x} ]; then
+  VIASH_PAR_OUTPUT_UNS_GENES_INDEX="nichecompass_genes_idx"
 fi
 if [ -z ${VIASH_PAR_OUTPUT_UNS_TARGET_GENES_INDEX+x} ]; then
  VIASH_PAR_OUTPUT_UNS_TARGET_GENES_INDEX="nichecompass_target_genes_idx"
@@ -2353,18 +2306,6 @@ if [ ! -z "$VIASH_PAR_INPUT_GP_MASK" ] && [ ! -e "$VIASH_PAR_INPUT_GP_MASK" ]; t
 fi

 # check whether parameters values are of the right type
-if [[ -n "$VIASH_PAR_N_SPATIAL_NEIGHBORS" ]]; then
-  if ! [[ "$VIASH_PAR_N_SPATIAL_NEIGHBORS" =~ ^[-+]?[0-9]+$ ]]; then
-    ViashError '--n_spatial_neighbors' has to be an integer. Use "--help" to get more information on the parameters.
-    exit 1
-  fi
-fi
-if [[ -n "$VIASH_PAR_DELAUNAY" ]]; then
-  if ! [[ "$VIASH_PAR_DELAUNAY" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
-    ViashError '--delaunay' has to be a boolean. Use "--help" to get more information on the parameters.
-    exit 1
-  fi
-fi
 if [[ -n "$VIASH_PAR_MIN_GENES_PER_GP" ]]; then
  if ! [[ "$VIASH_PAR_MIN_GENES_PER_GP" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--min_genes_per_gp' has to be an integer. Use "--help" to get more information on the parameters.
@@ -2989,18 +2930,6 @@ if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then
 fi

 # check whether value is belongs to a set of choices
-if [ ! -z "$VIASH_PAR_COORD_TYPE" ]; then
-  VIASH_PAR_COORD_TYPE_CHOICES=("generic;grid")
-  IFS=';'
-  set -f
-  if ! [[ ";${VIASH_PAR_COORD_TYPE_CHOICES[*]};" =~ ";$VIASH_PAR_COORD_TYPE;" ]]; then
-    ViashError '--coord_type' specified value of \'$VIASH_PAR_COORD_TYPE\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
-    exit 1
-  fi
-  set +f
-  unset IFS
-fi
-
 if [ ! -z "$VIASH_PAR_COVARIATE_EMBEDDING_INJECTION_LAYERS" ]; then
  VIASH_PAR_COVARIATE_EMBEDDING_INJECTION_LAYERS_CHOICES=("encoder;gene_expr_decoder;chrom_access_decoder")
  IFS=';'
@@ -3063,6 +2992,18 @@ if [ ! -z "$VIASH_PAR_CONV_LAYER_ENCODER" ]; then
  unset IFS
 fi

+if [ ! -z "$VIASH_PAR_OUTPUT_COMPRESSION" ]; then
+  VIASH_PAR_OUTPUT_COMPRESSION_CHOICES=("gzip;lzf")
+  IFS=';'
+  set -f
+  if ! [[ ";${VIASH_PAR_OUTPUT_COMPRESSION_CHOICES[*]};" =~ ";$VIASH_PAR_OUTPUT_COMPRESSION;" ]]; then
+    ViashError '--output_compression' specified value of \'$VIASH_PAR_OUTPUT_COMPRESSION\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
+    exit 1
+  fi
+  set +f
+  unset IFS
+fi
+
 # create parent directories of output files, if so desired
 if [ ! -z "$VIASH_PAR_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_OUTPUT")"
@@ -3185,9 +3126,6 @@ par = {
  'layer': $( if [ ! -z ${VIASH_PAR_LAYER+x} ]; then echo "r'${VIASH_PAR_LAYER//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'input_obsm_spatial_connectivities': $( if [ ! -z ${VIASH_PAR_INPUT_OBSM_SPATIAL_CONNECTIVITIES+x} ]; then echo "r'${VIASH_PAR_INPUT_OBSM_SPATIAL_CONNECTIVITIES//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'input_obs_covariates': $( if [ ! -z ${VIASH_PAR_INPUT_OBS_COVARIATES+x} ]; then echo "r'${VIASH_PAR_INPUT_OBS_COVARIATES//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
-  'coord_type': $( if [ ! -z ${VIASH_PAR_COORD_TYPE+x} ]; then echo "r'${VIASH_PAR_COORD_TYPE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
-  'n_spatial_neighbors': $( if [ ! -z ${VIASH_PAR_N_SPATIAL_NEIGHBORS+x} ]; then echo "int(r'${VIASH_PAR_N_SPATIAL_NEIGHBORS//\'/\'\"\'\"r\'}')"; else echo None; fi ),
-  'delaunay': $( if [ ! -z ${VIASH_PAR_DELAUNAY+x} ]; then echo "r'${VIASH_PAR_DELAUNAY//\'/\'\"\'\"r\'}'.lower() == 'true'"; else echo None; fi ),
  'min_genes_per_gp': $( if [ ! -z ${VIASH_PAR_MIN_GENES_PER_GP+x} ]; then echo "int(r'${VIASH_PAR_MIN_GENES_PER_GP//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'min_source_genes_per_gp': $( if [ ! -z ${VIASH_PAR_MIN_SOURCE_GENES_PER_GP+x} ]; then echo "int(r'${VIASH_PAR_MIN_SOURCE_GENES_PER_GP//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'min_target_genes_per_gp': $( if [ ! -z ${VIASH_PAR_MIN_TARGET_GENES_PER_GP+x} ]; then echo "int(r'${VIASH_PAR_MIN_TARGET_GENES_PER_GP//\'/\'\"\'\"r\'}')"; else echo None; fi ),
@@ -3244,12 +3182,13 @@ par = {
  'output_varm_gp_sources_mask': $( if [ ! -z ${VIASH_PAR_OUTPUT_VARM_GP_SOURCES_MASK+x} ]; then echo "r'${VIASH_PAR_OUTPUT_VARM_GP_SOURCES_MASK//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'output_uns_gp_names': $( if [ ! -z ${VIASH_PAR_OUTPUT_UNS_GP_NAMES+x} ]; then echo "r'${VIASH_PAR_OUTPUT_UNS_GP_NAMES//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'output_uns_active_gp_names': $( if [ ! -z ${VIASH_PAR_OUTPUT_UNS_ACTIVE_GP_NAMES+x} ]; then echo "r'${VIASH_PAR_OUTPUT_UNS_ACTIVE_GP_NAMES//\'/\'\"\'\"r\'}'"; else echo None; fi ),
-  'output_uns_gene_index': $( if [ ! -z ${VIASH_PAR_OUTPUT_UNS_GENE_INDEX+x} ]; then echo "r'${VIASH_PAR_OUTPUT_UNS_GENE_INDEX//\'/\'\"\'\"r\'}'"; else echo None; fi ),
+  'output_uns_genes_index': $( if [ ! -z ${VIASH_PAR_OUTPUT_UNS_GENES_INDEX+x} ]; then echo "r'${VIASH_PAR_OUTPUT_UNS_GENES_INDEX//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'output_uns_target_genes_index': $( if [ ! -z ${VIASH_PAR_OUTPUT_UNS_TARGET_GENES_INDEX+x} ]; then echo "r'${VIASH_PAR_OUTPUT_UNS_TARGET_GENES_INDEX//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'output_uns_source_genes_index': $( if [ ! -z ${VIASH_PAR_OUTPUT_UNS_SOURCE_GENES_INDEX+x} ]; then echo "r'${VIASH_PAR_OUTPUT_UNS_SOURCE_GENES_INDEX//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'output_uns_covariate_embeddings': $( if [ ! -z ${VIASH_PAR_OUTPUT_UNS_COVARIATE_EMBEDDINGS+x} ]; then echo "r'${VIASH_PAR_OUTPUT_UNS_COVARIATE_EMBEDDINGS//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'output_obsp_reconstructed_adj_edge_proba': $( if [ ! -z ${VIASH_PAR_OUTPUT_OBSP_RECONSTRUCTED_ADJ_EDGE_PROBA+x} ]; then echo "r'${VIASH_PAR_OUTPUT_OBSP_RECONSTRUCTED_ADJ_EDGE_PROBA//\'/\'\"\'\"r\'}'"; else echo None; fi ),
-  'output_obsp_agg_weights': $( if [ ! -z ${VIASH_PAR_OUTPUT_OBSP_AGG_WEIGHTS+x} ]; then echo "r'${VIASH_PAR_OUTPUT_OBSP_AGG_WEIGHTS//\'/\'\"\'\"r\'}'"; else echo None; fi )
+  'output_obsp_agg_weights': $( if [ ! -z ${VIASH_PAR_OUTPUT_OBSP_AGG_WEIGHTS+x} ]; then echo "r'${VIASH_PAR_OUTPUT_OBSP_AGG_WEIGHTS//\'/\'\"\'\"r\'}'"; else echo None; fi ),
+  'output_compression': $( if [ ! -z ${VIASH_PAR_OUTPUT_COMPRESSION+x} ]; then echo "r'${VIASH_PAR_OUTPUT_COMPRESSION//\'/\'\"\'\"r\'}'"; else echo None; fi )
 }
 meta = {
  'name': $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "r'${VIASH_META_NAME//\'/\'\"\'\"r\'}'"; else echo None; fi ),
@@ -3288,21 +3227,19 @@ logger.info("GPU enabled? %s", use_gpu)
 ## Read in data
 adata = mu.read_h5ad(par["input"], mod=par["modality"])

-# ## Compute spatial neighbor graph
-# logger.info("Computing spatial neighbor graph...")
-# # Compute connectivities and distances
-# sq.gr.spatial_neighbors(
-#     adata,
-#     coord_type=par["coord_type"],
-#     spatial_key=par["input_obsm_spatial_coords"],
-#     n_neighs=par["n_spatial_neighbors"],
-#     delaunay=par["delaunay"],
-# )
-
-# # Making the connectivity matrix symmetric
-# adata.obsp["spatial_connectivities"] = adata.obsp["spatial_connectivities"].maximum(
-#     adata.obsp["spatial_connectivities"].T
-# )
+# Counts need to be float32 to be processed by nichecompass model
+# See https://discuss.pytorch.org/t/runtimeerror-mat1-and-mat2-must-have-the-same-dtype/166759
+counts_dtype = (
+    adata.layers[par["layer"]].dtype if par["layer"] is not None else adata.X.dtype
+)
+if counts_dtype != "float32":
+    logger.info(
+        f"Converting count data to float32 from {counts_dtype} for model compatibility..."
+    )
+    if par["layer"] is not None:
+        adata.layers[par["layer"]] = adata.layers[par["layer"]].astype("float32")
+    else:
+        adata.X = adata.X.astype("float32")

 ## Add GP mask to data
 logger.info("Adding prior knowledge gene program mask to data...")
@@ -3315,7 +3252,7 @@ add_gps_from_gp_dict_to_adata(
    gp_targets_mask_key=par["output_varm_gp_targets_mask"],
    gp_sources_mask_key=par["output_varm_gp_sources_mask"],
    gp_names_key=par["output_uns_gp_names"],
-    genes_idx_key=par["output_uns_gene_index"],
+    genes_idx_key=par["output_uns_genes_index"],
    target_genes_idx_key=par["output_uns_target_genes_index"],
    source_genes_idx_key=par["output_uns_source_genes_index"],
    min_genes_per_gp=par["min_genes_per_gp"],
@@ -3338,12 +3275,12 @@ model = NicheCompass(
    gp_sources_mask_key=par["output_varm_gp_sources_mask"],
    latent_key=par["output_obsm_embedding"],
    cat_covariates_keys=par["input_obs_covariates"],
-    cat_covariates_no_edges=par["covariates_edges"],
+    cat_covariates_no_edges=par["covariate_edges"],
    cat_covariates_embeds_keys=par["output_uns_covariate_embeddings"],
-    cat_covariates_embeds_injection_layers=par["covariate_embedding_injection_layers"],
-    gene_idx_key=par["output_uns_gene_index"],
-    target_gene_idx_key=par["output_uns_target_genes_index"],
-    source_gene_idx_key=par["output_uns_source_genes_index"],
+    cat_covariates_embeds_injection=par["covariate_embedding_injection_layers"],
+    genes_idx_key=par["output_uns_genes_index"],
+    target_genes_idx_key=par["output_uns_target_genes_index"],
+    source_genes_idx_key=par["output_uns_source_genes_index"],
    recon_adj_key=par["output_obsp_reconstructed_adj_edge_proba"],
    agg_weights_key=par["output_obsp_agg_weights"],
    include_edge_recon_loss=par["include_edge_recon_loss"],
@@ -3364,7 +3301,6 @@ model = NicheCompass(
    encoder_use_bn=par["encoder_use_bn"],
    dropout_rate_encoder=par["dropout_rate_encoder"],
    dropout_rate_graph_decoder=par["dropout_rate_graph_decoder"],
-    cat_covariates_cats=par["cat_covariates_cats"],
    n_addon_gp=par["n_addon_gp"],
    cat_covariates_embeds_nums=par["cat_covariates_embeds_nums"],
    seed=par["random_state"],
@@ -3402,7 +3338,7 @@ model.train(
 ## Save model and data
 logger.info("Saving NicheCompass model and data...")
 mdata = mu.MuData({par["modality"]: adata})
-mdata.write_h5mu(par["output"])
+mdata.write_h5mu(par["output"], compression=par["output_compression"])

 model.save(par["output_model"], save_adata=False)
 VIASHMAIN
--- a/target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml
@@ -301,7 +301,7 @@ build_info:
  output: "target/nextflow/convert/from_cells2stats_to_h5mu"
  executable: "target/nextflow/convert/from_cells2stats_to_h5mu/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/convert/from_cells2stats_to_h5mu/main.nf
+++ b/target/nextflow/convert/from_cells2stats_to_h5mu/main.nf
@@ -3399,7 +3399,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_cells2stats_to_h5mu",
    "viash_version" : "0.9.4",
-    "git_commit" : "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831",
+    "git_commit" : "9151204629228da14d7c82f49f24c607efb9251e",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml
@@ -238,7 +238,7 @@ build_info:
  output: "target/nextflow/convert/from_cosmx_to_h5mu"
  executable: "target/nextflow/convert/from_cosmx_to_h5mu/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/convert/from_cosmx_to_h5mu/main.nf
+++ b/target/nextflow/convert/from_cosmx_to_h5mu/main.nf
@@ -3350,7 +3350,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_h5mu",
    "viash_version" : "0.9.4",
-    "git_commit" : "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831",
+    "git_commit" : "9151204629228da14d7c82f49f24c607efb9251e",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml
+++ b/target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml
@@ -234,7 +234,7 @@ build_info:
  output: "target/nextflow/convert/from_cosmx_to_spatialexperiment"
  executable: "target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf
+++ b/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf
@@ -3326,7 +3326,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_spatialexperiment",
    "viash_version" : "0.9.4",
-    "git_commit" : "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831",
+    "git_commit" : "9151204629228da14d7c82f49f24c607efb9251e",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml
+++ b/target/nextflow/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml
@@ -224,7 +224,7 @@ build_info:
  output: "target/nextflow/convert/from_h5mu_to_spatialexperiment"
  executable: "target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf
+++ b/target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf
@@ -3332,7 +3332,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_h5mu_to_spatialexperiment",
    "viash_version" : "0.9.4",
-    "git_commit" : "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831",
+    "git_commit" : "9151204629228da14d7c82f49f24c607efb9251e",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
@@ -221,7 +221,7 @@ build_info:
  output: "target/nextflow/convert/from_spatialdata_to_h5mu"
  executable: "target/nextflow/convert/from_spatialdata_to_h5mu/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf
+++ b/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf
@@ -3331,7 +3331,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_spatialdata_to_h5mu",
    "viash_version" : "0.9.4",
-    "git_commit" : "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831",
+    "git_commit" : "9151204629228da14d7c82f49f24c607efb9251e",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml
@@ -244,7 +244,7 @@ build_info:
  output: "target/nextflow/convert/from_xenium_to_h5mu"
  executable: "target/nextflow/convert/from_xenium_to_h5mu/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/convert/from_xenium_to_h5mu/main.nf
+++ b/target/nextflow/convert/from_xenium_to_h5mu/main.nf
@@ -3348,7 +3348,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_h5mu",
    "viash_version" : "0.9.4",
-    "git_commit" : "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831",
+    "git_commit" : "9151204629228da14d7c82f49f24c607efb9251e",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml
+++ b/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml
@@ -326,7 +326,7 @@ build_info:
  output: "target/nextflow/convert/from_xenium_to_spatialdata"
  executable: "target/nextflow/convert/from_xenium_to_spatialdata/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/convert/from_xenium_to_spatialdata/main.nf
+++ b/target/nextflow/convert/from_xenium_to_spatialdata/main.nf
@@ -3443,7 +3443,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialdata",
    "viash_version" : "0.9.4",
-    "git_commit" : "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831",
+    "git_commit" : "9151204629228da14d7c82f49f24c607efb9251e",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml
+++ b/target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml
@@ -224,7 +224,7 @@ build_info:
  output: "target/nextflow/convert/from_xenium_to_spatialexperiment"
  executable: "target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf
+++ b/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf
@@ -3315,7 +3315,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialexperiment",
    "viash_version" : "0.9.4",
-    "git_commit" : "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831",
+    "git_commit" : "9151204629228da14d7c82f49f24c607efb9251e",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/dataflow/obsp_block_concatenation/.config.vsh.yaml
+++ b/target/nextflow/dataflow/obsp_block_concatenation/.config.vsh.yaml
@@ -296,7 +296,7 @@ build_info:
  output: "target/nextflow/dataflow/obsp_block_concatenation"
  executable: "target/nextflow/dataflow/obsp_block_concatenation/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/dataflow/obsp_block_concatenation/main.nf
+++ b/target/nextflow/dataflow/obsp_block_concatenation/main.nf
@@ -3400,7 +3400,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/dataflow/obsp_block_concatenation",
    "viash_version" : "0.9.4",
-    "git_commit" : "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831",
+    "git_commit" : "9151204629228da14d7c82f49f24c607efb9251e",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml
+++ b/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml
@@ -426,7 +426,7 @@ build_info:
  output: "target/nextflow/mapping/spaceranger_count"
  executable: "target/nextflow/mapping/spaceranger_count/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/mapping/spaceranger_count/main.nf
+++ b/target/nextflow/mapping/spaceranger_count/main.nf
@@ -3548,7 +3548,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/mapping/spaceranger_count",
    "viash_version" : "0.9.4",
-    "git_commit" : "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831",
+    "git_commit" : "9151204629228da14d7c82f49f24c607efb9251e",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/neighbors/spatial_neighborhood_graph/.config.vsh.yaml
+++ b/target/nextflow/neighbors/spatial_neighborhood_graph/.config.vsh.yaml
@@ -1,5 +1,5 @@
-name: "neighbors"
-namespace: "spatial_neighborhood_graph"
+name: "spatial_neighborhood_graph"
+namespace: "neighbors"
 version: "niche-compass"
 authors:
 - name: "Dorien Roosen"
@@ -269,10 +269,10 @@ build_info:
  config: "src/neighbors/spatial_neighborhood_graph/config.vsh.yaml"
  runner: "nextflow"
  engine: "docker|native"
-  output: "target/nextflow/spatial_neighborhood_graph/neighbors"
-  executable: "target/nextflow/spatial_neighborhood_graph/neighbors/main.nf"
+  output: "target/nextflow/neighbors/spatial_neighborhood_graph"
+  executable: "target/nextflow/neighbors/spatial_neighborhood_graph/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/neighbors/spatial_neighborhood_graph/main.nf
+++ b/target/nextflow/neighbors/spatial_neighborhood_graph/main.nf
@@ -1,4 +1,4 @@
-// neighbors niche-compass
+// spatial_neighborhood_graph niche-compass
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3033,8 +3033,8 @@ nextflow.enable.dsl=2
 meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
-  "name" : "neighbors",
-  "namespace" : "spatial_neighborhood_graph",
+  "name" : "spatial_neighborhood_graph",
+  "namespace" : "neighbors",
  "version" : "niche-compass",
  "authors" : [
    {
@@ -3380,9 +3380,9 @@ meta = [
    "config" : "/workdir/root/repo/src/neighbors/spatial_neighborhood_graph/config.vsh.yaml",
    "runner" : "nextflow",
    "engine" : "docker|native",
-    "output" : "/workdir/root/repo/target/nextflow/spatial_neighborhood_graph/neighbors",
+    "output" : "/workdir/root/repo/target/nextflow/neighbors/spatial_neighborhood_graph",
    "viash_version" : "0.9.4",
-    "git_commit" : "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831",
+    "git_commit" : "9151204629228da14d7c82f49f24c607efb9251e",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
@@ -3884,7 +3884,7 @@ meta["defaults"] = [
  directives: readJsonBlob('''{
  "container" : {
    "registry" : "images.viash-hub.com",
-    "image" : "vsh/openpipeline_spatial/spatial_neighborhood_graph/neighbors",
+    "image" : "vsh/openpipeline_spatial/neighbors/spatial_neighborhood_graph",
    "tag" : "niche-compass"
  },
  "label" : [
--- a/target/nextflow/neighbors/spatial_neighborhood_graph/nextflow.config
+++ b/target/nextflow/neighbors/spatial_neighborhood_graph/nextflow.config
@@ -1,5 +1,5 @@
 manifest {
-  name = 'spatial_neighborhood_graph/neighbors'
+  name = 'neighbors/spatial_neighborhood_graph'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
  version = 'niche-compass'
--- a/target/nextflow/neighbors/spatial_neighborhood_graph/nextflow_labels.config
+++ b/target/nextflow/neighbors/spatial_neighborhood_graph/nextflow_labels.config
@@ -0,0 +1,68 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // CPU resources
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 4 }
+  withLabel: midcpu { cpus = 10 }
+  withLabel: highcpu { cpus = 20 }
+  
+  // Memory resources
+  withLabel: lowmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
+
+  // Disk space
+  // Nextflow apparently can't handle empty directives, i.e.
+  // withLabel: lowdisk {}
+  // so for that reason we have to add a dummy directive
+  withLabel: lowdisk {
+    dummyDirective = "dummyValue"
+  }
+  withLabel: middisk {
+    dummyDirective = "dummyValue"
+  }
+  withLabel: highdisk {
+    dummyDirective = "dummyValue"
+  }
+  withLabel: veryhighdisk {
+    dummyDirective = "dummyValue"
+  }
+  // NOTE: The above labels intentionally do not have an effect by default.
+  // The user should set the disk space requirements by adding the following
+  // to the compute environment:
+  //
+  // withLabel: lowdisk { disk = { 20.GB * task.attempt } }
+  // withLabel: middisk { disk = { 100.GB * task.attempt } }
+  // withLabel: highdisk { disk = { 200.GB * task.attempt } }
+  // withLabel: veryhighdisk { disk = { 500.GB * task.attempt } }
+}
+
+def get_memory(to_compare) {
+  if (!process.containsKey("maxMemory") || !process.maxMemory) {
+    return to_compare
+  }
+
+  try {
+    if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
+      return process.maxMemory
+    }
+    else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
+      return max_memory as nextflow.util.MemoryUnit
+    }
+    else {
+      return to_compare
+    }  
+  } catch (all) {
+        println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
+        System.exit(1)
+  }
+}
--- a/target/nextflow/neighbors/spatial_neighborhood_graph/nextflow_schema.json
+++ b/target/nextflow/neighbors/spatial_neighborhood_graph/nextflow_schema.json
@@ -1,6 +1,6 @@
 {
  "$schema": "https://json-schema.org/draft/2020-12/schema",
-  "title": "neighbors",
+  "title": "spatial_neighborhood_graph",
  "description": "Calculates a spatial neighborhood graph.",
  "type": "object",
  "$defs": {
--- a/target/nextflow/neighbors/spatial_neighborhood_graph/setup_logger.py
+++ b/target/nextflow/neighbors/spatial_neighborhood_graph/setup_logger.py
@@ -0,0 +1,12 @@
+def setup_logger():
+    import logging
+    from sys import stdout
+
+    logger = logging.getLogger()
+    logger.setLevel(logging.INFO)
+    console_handler = logging.StreamHandler(stdout)
+    logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
+    console_handler.setFormatter(logFormatter)
+    logger.addHandler(console_handler)
+
+    return logger
--- a/target/nextflow/nichecompass/gene_program_mask/.config.vsh.yaml
+++ b/target/nextflow/nichecompass/gene_program_mask/.config.vsh.yaml
@@ -0,0 +1,469 @@
+name: "gene_program_mask"
+namespace: "nichecompass"
+version: "niche-compass"
+authors:
+- name: "Dorien Roosen"
+  roles:
+  - "maintainer"
+  info:
+    role: "Core Team Member"
+    links:
+      email: "dorien@data-intuitive.com"
+      github: "dorien-er"
+      linkedin: "dorien-roosen"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--input_gene_orthologs_mapping_file"
+    description: "Path to a CSV file mapping human genes to mouse orthologs.\nRequired\
+      \ for the OmniPath and NicheNet masks if `--species mouse`.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--input_metabolite_enzymes"
+    description: "Path to the MeBocost metabolite-enzymes TSV file.\nRequired for\
+      \ generating the MeBocost gene program mask.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--input_metabolite_sensors"
+    description: "Path to the MeBocost metabolite-sensors TSV file.\nRequired for\
+      \ generating the MeBocost gene program mask.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Parameters"
+  arguments:
+  - type: "string"
+    name: "--species"
+    description: "Species of the organism (human or mouse)."
+    info: null
+    default:
+    - "human"
+    required: false
+    choices:
+    - "human"
+    - "mouse"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--create_omnipath_gene_program_mask"
+    description: "Whether to create the OmniPath gene program mask."
+    info: null
+    default:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--create_nichenet_gene_program_mask"
+    description: "Whether to create the NicheNet gene program mask."
+    info: null
+    default:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--create_mebocost_gene_program_mask"
+    description: "Whether to create the MeBocost gene program mask."
+    info: null
+    default:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--create_collectri_tf_gene_program_mask"
+    description: "Whether to create the CollecTRI TF gene program mask."
+    info: null
+    default:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--overlap_thresh_target_genes"
+    description: "The minimum ratio of target genes that need to overlap between a\
+      \ GP without source genes and another GP for the GP to be dropped.\nGene programs\
+      \ with different source genes are never combined or dropped.\n"
+    info: null
+    default:
+    - 1.0
+    required: false
+    min: 0.0
+    max: 1.0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Omnipath Parameters"
+  arguments:
+  - type: "integer"
+    name: "--omnipath_min_curation_effort"
+    description: "Minimum number of times an interaction has to be described in a\
+      \ paper and mentioned in a database to be included in the OmniPath gene programs."
+    info: null
+    default:
+    - 2
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "NicheNet Parameters"
+  arguments:
+  - type: "string"
+    name: "--nichenet_version"
+    description: "Version of the NicheNet ligand receptor network and ligand target\
+      \ gene regulatory potential matrix.\n´v2´ is an improved version of ´v1´, and\
+      \ has separate files for mouse and human.\n"
+    info: null
+    default:
+    - "v2"
+    required: false
+    choices:
+    - "v1"
+    - "v2"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--nichenet_keep_target_genes_ratio"
+    description: "Ratio of target genes that are kept compared to total target genes.\n\
+      This ratio is applied over the entire matrix (not on gene program level), and\
+      \ determines the ´all_gps_score_keep_threshold´, which will be used to filter\
+      \ target genes according to their regulatory potential scores.\n"
+    info: null
+    default:
+    - 1.0
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--nichenet_max_n_target_genes_per_gp"
+    description: "Maximum number of target genes per gene program. If a gene program\
+      \ has more target genes than ´max_n_target_genes_per_gp´, only the ´max_n_target_genes_per_gp´\
+      \ gene programs with the highest regulatory potential scores will be kept.\n\
+      Default value is chosen based on MultiNicheNet specification (s. Browaeys, R.\
+      \ et al. MultiNicheNet: a flexible framework for differential cell-cell communication\
+      \ analysis from multi-sample multi-condition single-cell transcriptomics data.\
+      \ bioRxiv (2023) doi:10.1101/2023.06.13.544751).\n"
+    info: null
+    default:
+    - 250
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "Path to the output gene program mask JSON file."
+    info: null
+    example:
+    - "gp_mask.json"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_omnipath_lr_network"
+    description: "Path to the output OmniPath ligand-receptor network CSV file."
+    info: null
+    example:
+    - "omnipath_lr_network.csv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_nichenet_lr_network"
+    description: "Path to the output NicheNet ligand-receptor network CSV file."
+    info: null
+    example:
+    - "nichenet_lr_network.csv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_nichenet_ligand_target_matrix"
+    description: "Path to the output NicheNet ligand-target gene regulatory potential\
+      \ matrix file."
+    info: null
+    example:
+    - "nichenet_ligand_target_matrix.csv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_collectri_tf_network"
+    description: "Path to the output CollecTRI TF-target gene regulatory potential\
+      \ network CSV file."
+    info: null
+    example:
+    - "collectri_tf_network.csv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_omnipath_gp_gene_count_distributions"
+    description: "Path to save the OmniPath gene program gene count distributions\
+      \ plot."
+    info: null
+    example:
+    - "omnipath_gp_gene_count_distributions.svg"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_nichenet_gp_gene_count_distributions"
+    description: "Path to save the NicheNet gene program gene count distributions\
+      \ plot."
+    info: null
+    example:
+    - "nichenet_gp_gene_count_distributions.svg"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_mebocost_gp_gene_count_distributions"
+    description: "Path to save the MeBocost gene program gene count distributions\
+      \ plot."
+    info: null
+    example:
+    - "mebocost_gp_gene_count_distributions.svg"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_collectri_tf_gp_gene_count_distributions"
+    description: "Path to save the CollecTRI TF gene program gene count distributions\
+      \ plot."
+    info: null
+    example:
+    - "collectri_tf_gp_gene_count_distributions.svg"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "python_script"
+  path: "script.py"
+  is_executable: true
+- type: "file"
+  path: "setup_logger.py"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
+description: "Generation of a prior knowledge gene program mask for NicheCompass."
+test_resources:
+- type: "python_script"
+  path: "test.py"
+  is_executable: true
+- type: "file"
+  path: "niche"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+repositories:
+- type: "vsh"
+  name: "openpipeline"
+  repo: "openpipeline"
+  tag: "v3.0.0"
+links:
+  repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
+  docker_registry: "ghcr.io"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    label:
+    - "lowcpu"
+    - "lowmem"
+    - "lowdisk"
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "nvidia/cuda:12.4.1-cudnn-devel-ubuntu22.04"
+  target_registry: "images.viash-hub.com"
+  target_tag: "niche-compass"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "libhdf5-dev"
+    - "python3-pip"
+    - "python3-dev"
+    - "python-is-python3"
+    interactive: false
+  - type: "docker"
+    run:
+    - "pip install torch --index-url https://download.pytorch.org/whl/cu124 \\\n&&\
+      \ pip install pyg_lib torch-scatter torch-sparse -f https://data.pyg.org/whl/torch-2.6.0+cu124.html\
+      \   \n"
+  - type: "python"
+    user: false
+    packages:
+    - "numpy<2"
+    - "nichecompass"
+    upgrade: true
+  test_setup:
+  - type: "python"
+    user: false
+    packages:
+    - "viashpy==0.9.0"
+    upgrade: true
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/nichecompass/gene_program_mask/config.vsh.yaml"
+  runner: "nextflow"
+  engine: "docker|native"
+  output: "target/nextflow/nichecompass/gene_program_mask"
+  executable: "target/nextflow/nichecompass/gene_program_mask/main.nf"
+  viash_version: "0.9.4"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
+  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
+package_config:
+  name: "openpipeline_spatial"
+  version: "niche-compass"
+  info:
+    test_resources:
+    - type: "s3"
+      path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
+      dest: "resources_test"
+  repositories:
+  - type: "vsh"
+    name: "openpipeline"
+    repo: "openpipeline"
+    tag: "v3.0.0"
+  viash_version: "0.9.4"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
+    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    )'"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'niche-compass'"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
+    docker_registry: "ghcr.io"
--- a/target/nextflow/nichecompass/gene_program_mask/main.nf
+++ b/target/nextflow/nichecompass/gene_program_mask/main.nf
--- a/target/nextflow/nichecompass/gene_program_mask/nextflow.config
+++ b/target/nextflow/nichecompass/gene_program_mask/nextflow.config
@@ -0,0 +1,126 @@
+manifest {
+  name = 'nichecompass/gene_program_mask'
+  mainScript = 'main.nf'
+  nextflowVersion = '!>=20.12.1-edge'
+  version = 'niche-compass'
+  description = 'Generation of a prior knowledge gene program mask for NicheCompass.'
+  author = 'Dorien Roosen'
+}
+
+process.container = 'nextflow/bash:latest'
+
+// detect tempdir
+tempDir = java.nio.file.Paths.get(
+  System.getenv('NXF_TEMP') ?:
+    System.getenv('VIASH_TEMP') ?: 
+    System.getenv('TEMPDIR') ?: 
+    System.getenv('TMPDIR') ?: 
+    '/tmp'
+).toAbsolutePath()
+
+profiles {
+  no_publish {
+    process {
+      withName: '.*' {
+        publishDir = [
+          enabled: false
+        ]
+      }
+    }
+  }
+  mount_temp {
+    docker.temp            = tempDir
+    podman.temp            = tempDir
+    charliecloud.temp      = tempDir
+  }
+  docker {
+    docker.enabled         = true
+    // docker.userEmulation   = true
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  singularity {
+    singularity.enabled    = true
+    singularity.autoMounts = true
+    docker.enabled         = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  podman {
+    podman.enabled         = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  shifter {
+    shifter.enabled        = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    charliecloud.enabled   = false
+  }
+  charliecloud {
+    charliecloud.enabled   = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+  }
+}
+
+process{
+  withLabel: mem1gb { memory = 1000000000.B }
+  withLabel: mem2gb { memory = 2000000000.B }
+  withLabel: mem5gb { memory = 5000000000.B }
+  withLabel: mem10gb { memory = 10000000000.B }
+  withLabel: mem20gb { memory = 20000000000.B }
+  withLabel: mem50gb { memory = 50000000000.B }
+  withLabel: mem100gb { memory = 100000000000.B }
+  withLabel: mem200gb { memory = 200000000000.B }
+  withLabel: mem500gb { memory = 500000000000.B }
+  withLabel: mem1tb { memory = 1000000000000.B }
+  withLabel: mem2tb { memory = 2000000000000.B }
+  withLabel: mem5tb { memory = 5000000000000.B }
+  withLabel: mem10tb { memory = 10000000000000.B }
+  withLabel: mem20tb { memory = 20000000000000.B }
+  withLabel: mem50tb { memory = 50000000000000.B }
+  withLabel: mem100tb { memory = 100000000000000.B }
+  withLabel: mem200tb { memory = 200000000000000.B }
+  withLabel: mem500tb { memory = 500000000000000.B }
+  withLabel: mem1gib { memory = 1073741824.B }
+  withLabel: mem2gib { memory = 2147483648.B }
+  withLabel: mem4gib { memory = 4294967296.B }
+  withLabel: mem8gib { memory = 8589934592.B }
+  withLabel: mem16gib { memory = 17179869184.B }
+  withLabel: mem32gib { memory = 34359738368.B }
+  withLabel: mem64gib { memory = 68719476736.B }
+  withLabel: mem128gib { memory = 137438953472.B }
+  withLabel: mem256gib { memory = 274877906944.B }
+  withLabel: mem512gib { memory = 549755813888.B }
+  withLabel: mem1tib { memory = 1099511627776.B }
+  withLabel: mem2tib { memory = 2199023255552.B }
+  withLabel: mem4tib { memory = 4398046511104.B }
+  withLabel: mem8tib { memory = 8796093022208.B }
+  withLabel: mem16tib { memory = 17592186044416.B }
+  withLabel: mem32tib { memory = 35184372088832.B }
+  withLabel: mem64tib { memory = 70368744177664.B }
+  withLabel: mem128tib { memory = 140737488355328.B }
+  withLabel: mem256tib { memory = 281474976710656.B }
+  withLabel: mem512tib { memory = 562949953421312.B }
+  withLabel: cpu1 { cpus = 1 }
+  withLabel: cpu2 { cpus = 2 }
+  withLabel: cpu5 { cpus = 5 }
+  withLabel: cpu10 { cpus = 10 }
+  withLabel: cpu20 { cpus = 20 }
+  withLabel: cpu50 { cpus = 50 }
+  withLabel: cpu100 { cpus = 100 }
+  withLabel: cpu200 { cpus = 200 }
+  withLabel: cpu500 { cpus = 500 }
+  withLabel: cpu1000 { cpus = 1000 }
+}
+
+includeConfig("nextflow_labels.config")
--- a/target/nextflow/nichecompass/gene_program_mask/nextflow_labels.config
+++ b/target/nextflow/nichecompass/gene_program_mask/nextflow_labels.config
@@ -0,0 +1,68 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // CPU resources
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 4 }
+  withLabel: midcpu { cpus = 10 }
+  withLabel: highcpu { cpus = 20 }
+  
+  // Memory resources
+  withLabel: lowmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
+
+  // Disk space
+  // Nextflow apparently can't handle empty directives, i.e.
+  // withLabel: lowdisk {}
+  // so for that reason we have to add a dummy directive
+  withLabel: lowdisk {
+    dummyDirective = "dummyValue"
+  }
+  withLabel: middisk {
+    dummyDirective = "dummyValue"
+  }
+  withLabel: highdisk {
+    dummyDirective = "dummyValue"
+  }
+  withLabel: veryhighdisk {
+    dummyDirective = "dummyValue"
+  }
+  // NOTE: The above labels intentionally do not have an effect by default.
+  // The user should set the disk space requirements by adding the following
+  // to the compute environment:
+  //
+  // withLabel: lowdisk { disk = { 20.GB * task.attempt } }
+  // withLabel: middisk { disk = { 100.GB * task.attempt } }
+  // withLabel: highdisk { disk = { 200.GB * task.attempt } }
+  // withLabel: veryhighdisk { disk = { 500.GB * task.attempt } }
+}
+
+def get_memory(to_compare) {
+  if (!process.containsKey("maxMemory") || !process.maxMemory) {
+    return to_compare
+  }
+
+  try {
+    if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
+      return process.maxMemory
+    }
+    else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
+      return max_memory as nextflow.util.MemoryUnit
+    }
+    else {
+      return to_compare
+    }  
+  } catch (all) {
+        println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
+        System.exit(1)
+  }
+}
--- a/target/nextflow/nichecompass/gene_program_mask/nextflow_schema.json
+++ b/target/nextflow/nichecompass/gene_program_mask/nextflow_schema.json
@@ -0,0 +1,224 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "title": "gene_program_mask",
+  "description": "Generation of a prior knowledge gene program mask for NicheCompass.",
+  "type": "object",
+  "$defs": {
+    "inputs": {
+      "title": "Inputs",
+      "type": "object",
+      "description": "No description",
+      "properties": {
+        "input_gene_orthologs_mapping_file": {
+          "type": "string",
+          "format": "path",
+          "description": "Path to a CSV file mapping human genes to mouse orthologs.\nRequired for the OmniPath and NicheNet masks if `--species mouse`.\n",
+          "help_text": "Type: `file`, multiple: `False`, direction: `input`. "
+        },
+        "input_metabolite_enzymes": {
+          "type": "string",
+          "format": "path",
+          "description": "Path to the MeBocost metabolite-enzymes TSV file.\nRequired for generating the MeBocost gene program mask.\n",
+          "help_text": "Type: `file`, multiple: `False`, direction: `input`. "
+        },
+        "input_metabolite_sensors": {
+          "type": "string",
+          "format": "path",
+          "description": "Path to the MeBocost metabolite-sensors TSV file.\nRequired for generating the MeBocost gene program mask.\n",
+          "help_text": "Type: `file`, multiple: `False`, direction: `input`. "
+        }
+      }
+    },
+    "outputs": {
+      "title": "Outputs",
+      "type": "object",
+      "description": "No description",
+      "properties": {
+        "output": {
+          "type": "string",
+          "format": "path",
+          "description": "Path to the output gene program mask JSON file.",
+          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.json\"`, direction: `output`, example: `\"gp_mask.json\"`. ",
+          "default": "$id.$key.output.json"
+        },
+        "output_omnipath_lr_network": {
+          "type": "string",
+          "format": "path",
+          "description": "Path to the output OmniPath ligand-receptor network CSV file.",
+          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_omnipath_lr_network.csv\"`, direction: `output`, example: `\"omnipath_lr_network.csv\"`. ",
+          "default": "$id.$key.output_omnipath_lr_network.csv"
+        },
+        "output_nichenet_lr_network": {
+          "type": "string",
+          "format": "path",
+          "description": "Path to the output NicheNet ligand-receptor network CSV file.",
+          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_nichenet_lr_network.csv\"`, direction: `output`, example: `\"nichenet_lr_network.csv\"`. ",
+          "default": "$id.$key.output_nichenet_lr_network.csv"
+        },
+        "output_nichenet_ligand_target_matrix": {
+          "type": "string",
+          "format": "path",
+          "description": "Path to the output NicheNet ligand-target gene regulatory potential matrix file.",
+          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_nichenet_ligand_target_matrix.csv\"`, direction: `output`, example: `\"nichenet_ligand_target_matrix.csv\"`. ",
+          "default": "$id.$key.output_nichenet_ligand_target_matrix.csv"
+        },
+        "output_collectri_tf_network": {
+          "type": "string",
+          "format": "path",
+          "description": "Path to the output CollecTRI TF-target gene regulatory potential network CSV file.",
+          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_collectri_tf_network.csv\"`, direction: `output`, example: `\"collectri_tf_network.csv\"`. ",
+          "default": "$id.$key.output_collectri_tf_network.csv"
+        },
+        "output_omnipath_gp_gene_count_distributions": {
+          "type": "string",
+          "format": "path",
+          "description": "Path to save the OmniPath gene program gene count distributions plot.",
+          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_omnipath_gp_gene_count_distributions.svg\"`, direction: `output`, example: `\"omnipath_gp_gene_count_distributions.svg\"`. ",
+          "default": "$id.$key.output_omnipath_gp_gene_count_distributions.svg"
+        },
+        "output_nichenet_gp_gene_count_distributions": {
+          "type": "string",
+          "format": "path",
+          "description": "Path to save the NicheNet gene program gene count distributions plot.",
+          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_nichenet_gp_gene_count_distributions.svg\"`, direction: `output`, example: `\"nichenet_gp_gene_count_distributions.svg\"`. ",
+          "default": "$id.$key.output_nichenet_gp_gene_count_distributions.svg"
+        },
+        "output_mebocost_gp_gene_count_distributions": {
+          "type": "string",
+          "format": "path",
+          "description": "Path to save the MeBocost gene program gene count distributions plot.",
+          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_mebocost_gp_gene_count_distributions.svg\"`, direction: `output`, example: `\"mebocost_gp_gene_count_distributions.svg\"`. ",
+          "default": "$id.$key.output_mebocost_gp_gene_count_distributions.svg"
+        },
+        "output_collectri_tf_gp_gene_count_distributions": {
+          "type": "string",
+          "format": "path",
+          "description": "Path to save the CollecTRI TF gene program gene count distributions plot.",
+          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_collectri_tf_gp_gene_count_distributions.svg\"`, direction: `output`, example: `\"collectri_tf_gp_gene_count_distributions.svg\"`. ",
+          "default": "$id.$key.output_collectri_tf_gp_gene_count_distributions.svg"
+        }
+      }
+    },
+    "parameters": {
+      "title": "Parameters",
+      "type": "object",
+      "description": "No description",
+      "properties": {
+        "species": {
+          "type": "string",
+          "description": "Species of the organism (human or mouse).",
+          "help_text": "Type: `string`, multiple: `False`, default: `\"human\"`, choices: ``human`, `mouse``. ",
+          "enum": [
+            "human",
+            "mouse"
+          ],
+          "default": "human"
+        },
+        "create_omnipath_gene_program_mask": {
+          "type": "boolean",
+          "description": "Whether to create the OmniPath gene program mask.",
+          "help_text": "Type: `boolean`, multiple: `False`, default: `true`. ",
+          "default": true
+        },
+        "create_nichenet_gene_program_mask": {
+          "type": "boolean",
+          "description": "Whether to create the NicheNet gene program mask.",
+          "help_text": "Type: `boolean`, multiple: `False`, default: `true`. ",
+          "default": true
+        },
+        "create_mebocost_gene_program_mask": {
+          "type": "boolean",
+          "description": "Whether to create the MeBocost gene program mask.",
+          "help_text": "Type: `boolean`, multiple: `False`, default: `true`. ",
+          "default": true
+        },
+        "create_collectri_tf_gene_program_mask": {
+          "type": "boolean",
+          "description": "Whether to create the CollecTRI TF gene program mask.",
+          "help_text": "Type: `boolean`, multiple: `False`, default: `true`. ",
+          "default": true
+        },
+        "overlap_thresh_target_genes": {
+          "type": "number",
+          "description": "The minimum ratio of target genes that need to overlap between a GP without source genes and another GP for the GP to be dropped.\nGene programs with different source genes are never combined or dropped.\n",
+          "help_text": "Type: `double`, multiple: `False`, default: `1.0`. ",
+          "default": 1.0
+        }
+      }
+    },
+    "omnipath parameters": {
+      "title": "Omnipath Parameters",
+      "type": "object",
+      "description": "No description",
+      "properties": {
+        "omnipath_min_curation_effort": {
+          "type": "integer",
+          "description": "Minimum number of times an interaction has to be described in a paper and mentioned in a database to be included in the OmniPath gene programs.",
+          "help_text": "Type: `integer`, multiple: `False`, default: `2`. ",
+          "default": 2
+        }
+      }
+    },
+    "nichenet parameters": {
+      "title": "NicheNet Parameters",
+      "type": "object",
+      "description": "No description",
+      "properties": {
+        "nichenet_version": {
+          "type": "string",
+          "description": "Version of the NicheNet ligand receptor network and ligand target gene regulatory potential matrix.\n´v2´ is an improved version of ´v1´, and has separate files for mouse and human.\n",
+          "help_text": "Type: `string`, multiple: `False`, default: `\"v2\"`, choices: ``v1`, `v2``. ",
+          "enum": [
+            "v1",
+            "v2"
+          ],
+          "default": "v2"
+        },
+        "nichenet_keep_target_genes_ratio": {
+          "type": "number",
+          "description": "Ratio of target genes that are kept compared to total target genes.\nThis ratio is applied over the entire matrix (not on gene program level), and determines the ´all_gps_score_keep_threshold´, which will be used to filter target genes according to their regulatory potential scores.\n",
+          "help_text": "Type: `double`, multiple: `False`, default: `1.0`. ",
+          "default": 1.0
+        },
+        "nichenet_max_n_target_genes_per_gp": {
+          "type": "integer",
+          "description": "Maximum number of target genes per gene program",
+          "help_text": "Type: `integer`, multiple: `False`, default: `250`. ",
+          "default": 250
+        }
+      }
+    },
+    "nextflow input-output arguments": {
+      "title": "Nextflow input-output arguments",
+      "type": "object",
+      "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
+      "properties": {
+        "publish_dir": {
+          "type": "string",
+          "description": "Path to an output directory.",
+          "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
+        }
+      }
+    }
+  },
+  "allOf": [
+    {
+      "$ref": "#/$defs/inputs"
+    },
+    {
+      "$ref": "#/$defs/outputs"
+    },
+    {
+      "$ref": "#/$defs/parameters"
+    },
+    {
+      "$ref": "#/$defs/omnipath parameters"
+    },
+    {
+      "$ref": "#/$defs/nichenet parameters"
+    },
+    {
+      "$ref": "#/$defs/nextflow input-output arguments"
+    }
+  ]
+}
--- a/target/nextflow/nichecompass/gene_program_mask/setup_logger.py
+++ b/target/nextflow/nichecompass/gene_program_mask/setup_logger.py
@@ -0,0 +1,12 @@
+def setup_logger():
+    import logging
+    from sys import stdout
+
+    logger = logging.getLogger()
+    logger.setLevel(logging.INFO)
+    console_handler = logging.StreamHandler(stdout)
+    logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
+    console_handler.setFormatter(logFormatter)
+    logger.addHandler(console_handler)
+
+    return logger
--- a/target/nextflow/nichecompass/nichecompass/.config.vsh.yaml
+++ b/target/nextflow/nichecompass/nichecompass/.config.vsh.yaml
@@ -83,45 +83,6 @@ argument_groups:
    direction: "input"
    multiple: true
    multiple_sep: ";"
- name: "Spatial Neighbors Calculation"
-  arguments:
-  - type: "string"
-    name: "--coord_type"
-    description: "Type of coordinate system. Valid options are:\n`grid` - grid coordinates.\n\
-      `generic` - generic coordinates.\nIf not provided, `grid` is used if `--input_obsm_spatial_coords`\
-      \ is in --input .uns with `--n_neighs` = 6 (Visium), otherwise `generic` is\
-      \ used.\n"
-    info: null
-    required: false
-    choices:
-    - "generic"
-    - "grid"
-    direction: "input"
-    multiple: false
-    multiple_sep: ";"
-  - type: "integer"
-    name: "--n_spatial_neighbors"
-    description: "Depending on `--coord_type`:\n`grid` - number of neighboring tiles.\n\
-      `generic` - number of neighborhoods for non-grid data. Only used when `--delaunay\
-      \ False`.\n"
-    info: null
-    default:
-    - 6
-    required: false
-    direction: "input"
-    multiple: false
-    multiple_sep: ";"
-  - type: "boolean"
-    name: "--delaunay"
-    description: "Whether to use Delaunay triangulation to determine spatial neighborhood\
-      \ graph.\nOnly used when `--coord_type generic`.\n"
-    info: null
-    default:
-    - false
-    required: false
-    direction: "input"
-    multiple: false
-    multiple_sep: ";"
 - name: "Gene Program Mask"
  arguments:
  - type: "integer"
@@ -807,12 +768,12 @@ argument_groups:
    multiple: false
    multiple_sep: ";"
  - type: "string"
-    name: "--output_uns_gene_index"
+    name: "--output_uns_genes_index"
    description: "Key of the uns field where the index of a concatenated vector of\
      \ target and source genes that are in the gene program masks will be stored.\n"
    info: null
    default:
-    - "nichecompass_gene_idx"
+    - "nichecompass_genes_idx"
    required: false
    direction: "input"
    multiple: false
@@ -870,6 +831,20 @@ argument_groups:
    direction: "input"
    multiple: false
    multiple_sep: ";"
+  - type: "string"
+    name: "--output_compression"
+    description: "Compression format to use for the output AnnData and/or Mudata objects.\n\
+      By default no compression is applied.\n"
+    info: null
+    example:
+    - "gzip"
+    required: false
+    choices:
+    - "gzip"
+    - "lzf"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
 resources:
 - type: "python_script"
  path: "script.py"
@@ -1028,7 +1003,7 @@ build_info:
  output: "target/nextflow/nichecompass/nichecompass"
  executable: "target/nextflow/nichecompass/nichecompass/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/nichecompass/nichecompass/main.nf
+++ b/target/nextflow/nichecompass/nichecompass/main.nf
@@ -3132,48 +3132,6 @@ meta = [
        }
      ]
    },
-    {
-      "name" : "Spatial Neighbors Calculation",
-      "arguments" : [
-        {
-          "type" : "string",
-          "name" : "--coord_type",
-          "description" : "Type of coordinate system. Valid options are:\n`grid` - grid coordinates.\n`generic` - generic coordinates.\nIf not provided, `grid` is used if `--input_obsm_spatial_coords` is in --input .uns with `--n_neighs` = 6 (Visium), otherwise `generic` is used.\n",
-          "required" : false,
-          "choices" : [
-            "generic",
-            "grid"
-          ],
-          "direction" : "input",
-          "multiple" : false,
-          "multiple_sep" : ";"
-        },
-        {
-          "type" : "integer",
-          "name" : "--n_spatial_neighbors",
-          "description" : "Depending on `--coord_type`:\n`grid` - number of neighboring tiles.\n`generic` - number of neighborhoods for non-grid data. Only used when `--delaunay False`.\n",
-          "default" : [
-            6
-          ],
-          "required" : false,
-          "direction" : "input",
-          "multiple" : false,
-          "multiple_sep" : ";"
-        },
-        {
-          "type" : "boolean",
-          "name" : "--delaunay",
-          "description" : "Whether to use Delaunay triangulation to determine spatial neighborhood graph.\nOnly used when `--coord_type generic`.\n",
-          "default" : [
-            false
-          ],
-          "required" : false,
-          "direction" : "input",
-          "multiple" : false,
-          "multiple_sep" : ";"
-        }
-      ]
-    },
    {
      "name" : "Gene Program Mask",
      "arguments" : [
@@ -3889,10 +3847,10 @@ meta = [
        },
        {
          "type" : "string",
-          "name" : "--output_uns_gene_index",
+          "name" : "--output_uns_genes_index",
          "description" : "Key of the uns field where the index of a concatenated vector of target and source genes that are in the gene program masks will be stored.\n",
          "default" : [
-            "nichecompass_gene_idx"
+            "nichecompass_genes_idx"
          ],
          "required" : false,
          "direction" : "input",
@@ -3955,6 +3913,22 @@ meta = [
          "direction" : "input",
          "multiple" : false,
          "multiple_sep" : ";"
+        },
+        {
+          "type" : "string",
+          "name" : "--output_compression",
+          "description" : "Compression format to use for the output AnnData and/or Mudata objects.\nBy default no compression is applied.\n",
+          "example" : [
+            "gzip"
+          ],
+          "required" : false,
+          "choices" : [
+            "gzip",
+            "lzf"
+          ],
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
        }
      ]
    }
@@ -4164,7 +4138,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/nichecompass/nichecompass",
    "viash_version" : "0.9.4",
-    "git_commit" : "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831",
+    "git_commit" : "9151204629228da14d7c82f49f24c607efb9251e",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
@@ -4231,9 +4205,6 @@ par = {
  'layer': $( if [ ! -z ${VIASH_PAR_LAYER+x} ]; then echo "r'${VIASH_PAR_LAYER//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ),
  'input_obsm_spatial_connectivities': $( if [ ! -z ${VIASH_PAR_INPUT_OBSM_SPATIAL_CONNECTIVITIES+x} ]; then echo "r'${VIASH_PAR_INPUT_OBSM_SPATIAL_CONNECTIVITIES//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ),
  'input_obs_covariates': $( if [ ! -z ${VIASH_PAR_INPUT_OBS_COVARIATES+x} ]; then echo "r'${VIASH_PAR_INPUT_OBS_COVARIATES//\\'/\\'\\"\\'\\"r\\'}'.split(';')"; else echo None; fi ),
-  'coord_type': $( if [ ! -z ${VIASH_PAR_COORD_TYPE+x} ]; then echo "r'${VIASH_PAR_COORD_TYPE//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ),
-  'n_spatial_neighbors': $( if [ ! -z ${VIASH_PAR_N_SPATIAL_NEIGHBORS+x} ]; then echo "int(r'${VIASH_PAR_N_SPATIAL_NEIGHBORS//\\'/\\'\\"\\'\\"r\\'}')"; else echo None; fi ),
-  'delaunay': $( if [ ! -z ${VIASH_PAR_DELAUNAY+x} ]; then echo "r'${VIASH_PAR_DELAUNAY//\\'/\\'\\"\\'\\"r\\'}'.lower() == 'true'"; else echo None; fi ),
  'min_genes_per_gp': $( if [ ! -z ${VIASH_PAR_MIN_GENES_PER_GP+x} ]; then echo "int(r'${VIASH_PAR_MIN_GENES_PER_GP//\\'/\\'\\"\\'\\"r\\'}')"; else echo None; fi ),
  'min_source_genes_per_gp': $( if [ ! -z ${VIASH_PAR_MIN_SOURCE_GENES_PER_GP+x} ]; then echo "int(r'${VIASH_PAR_MIN_SOURCE_GENES_PER_GP//\\'/\\'\\"\\'\\"r\\'}')"; else echo None; fi ),
  'min_target_genes_per_gp': $( if [ ! -z ${VIASH_PAR_MIN_TARGET_GENES_PER_GP+x} ]; then echo "int(r'${VIASH_PAR_MIN_TARGET_GENES_PER_GP//\\'/\\'\\"\\'\\"r\\'}')"; else echo None; fi ),
@@ -4290,12 +4261,13 @@ par = {
  'output_varm_gp_sources_mask': $( if [ ! -z ${VIASH_PAR_OUTPUT_VARM_GP_SOURCES_MASK+x} ]; then echo "r'${VIASH_PAR_OUTPUT_VARM_GP_SOURCES_MASK//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ),
  'output_uns_gp_names': $( if [ ! -z ${VIASH_PAR_OUTPUT_UNS_GP_NAMES+x} ]; then echo "r'${VIASH_PAR_OUTPUT_UNS_GP_NAMES//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ),
  'output_uns_active_gp_names': $( if [ ! -z ${VIASH_PAR_OUTPUT_UNS_ACTIVE_GP_NAMES+x} ]; then echo "r'${VIASH_PAR_OUTPUT_UNS_ACTIVE_GP_NAMES//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ),
-  'output_uns_gene_index': $( if [ ! -z ${VIASH_PAR_OUTPUT_UNS_GENE_INDEX+x} ]; then echo "r'${VIASH_PAR_OUTPUT_UNS_GENE_INDEX//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ),
+  'output_uns_genes_index': $( if [ ! -z ${VIASH_PAR_OUTPUT_UNS_GENES_INDEX+x} ]; then echo "r'${VIASH_PAR_OUTPUT_UNS_GENES_INDEX//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ),
  'output_uns_target_genes_index': $( if [ ! -z ${VIASH_PAR_OUTPUT_UNS_TARGET_GENES_INDEX+x} ]; then echo "r'${VIASH_PAR_OUTPUT_UNS_TARGET_GENES_INDEX//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ),
  'output_uns_source_genes_index': $( if [ ! -z ${VIASH_PAR_OUTPUT_UNS_SOURCE_GENES_INDEX+x} ]; then echo "r'${VIASH_PAR_OUTPUT_UNS_SOURCE_GENES_INDEX//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ),
  'output_uns_covariate_embeddings': $( if [ ! -z ${VIASH_PAR_OUTPUT_UNS_COVARIATE_EMBEDDINGS+x} ]; then echo "r'${VIASH_PAR_OUTPUT_UNS_COVARIATE_EMBEDDINGS//\\'/\\'\\"\\'\\"r\\'}'.split(';')"; else echo None; fi ),
  'output_obsp_reconstructed_adj_edge_proba': $( if [ ! -z ${VIASH_PAR_OUTPUT_OBSP_RECONSTRUCTED_ADJ_EDGE_PROBA+x} ]; then echo "r'${VIASH_PAR_OUTPUT_OBSP_RECONSTRUCTED_ADJ_EDGE_PROBA//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ),
-  'output_obsp_agg_weights': $( if [ ! -z ${VIASH_PAR_OUTPUT_OBSP_AGG_WEIGHTS+x} ]; then echo "r'${VIASH_PAR_OUTPUT_OBSP_AGG_WEIGHTS//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi )
+  'output_obsp_agg_weights': $( if [ ! -z ${VIASH_PAR_OUTPUT_OBSP_AGG_WEIGHTS+x} ]; then echo "r'${VIASH_PAR_OUTPUT_OBSP_AGG_WEIGHTS//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ),
+  'output_compression': $( if [ ! -z ${VIASH_PAR_OUTPUT_COMPRESSION+x} ]; then echo "r'${VIASH_PAR_OUTPUT_COMPRESSION//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi )
 }
 meta = {
  'name': $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "r'${VIASH_META_NAME//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ),
@@ -4334,21 +4306,19 @@ logger.info("GPU enabled? %s", use_gpu)
 ## Read in data
 adata = mu.read_h5ad(par["input"], mod=par["modality"])

-# ## Compute spatial neighbor graph
-# logger.info("Computing spatial neighbor graph...")
-# # Compute connectivities and distances
-# sq.gr.spatial_neighbors(
-#     adata,
-#     coord_type=par["coord_type"],
-#     spatial_key=par["input_obsm_spatial_coords"],
-#     n_neighs=par["n_spatial_neighbors"],
-#     delaunay=par["delaunay"],
-# )
-
-# # Making the connectivity matrix symmetric
-# adata.obsp["spatial_connectivities"] = adata.obsp["spatial_connectivities"].maximum(
-#     adata.obsp["spatial_connectivities"].T
-# )
+# Counts need to be float32 to be processed by nichecompass model
+# See https://discuss.pytorch.org/t/runtimeerror-mat1-and-mat2-must-have-the-same-dtype/166759
+counts_dtype = (
+    adata.layers[par["layer"]].dtype if par["layer"] is not None else adata.X.dtype
+)
+if counts_dtype != "float32":
+    logger.info(
+        f"Converting count data to float32 from {counts_dtype} for model compatibility..."
+    )
+    if par["layer"] is not None:
+        adata.layers[par["layer"]] = adata.layers[par["layer"]].astype("float32")
+    else:
+        adata.X = adata.X.astype("float32")

 ## Add GP mask to data
 logger.info("Adding prior knowledge gene program mask to data...")
@@ -4361,7 +4331,7 @@ add_gps_from_gp_dict_to_adata(
    gp_targets_mask_key=par["output_varm_gp_targets_mask"],
    gp_sources_mask_key=par["output_varm_gp_sources_mask"],
    gp_names_key=par["output_uns_gp_names"],
-    genes_idx_key=par["output_uns_gene_index"],
+    genes_idx_key=par["output_uns_genes_index"],
    target_genes_idx_key=par["output_uns_target_genes_index"],
    source_genes_idx_key=par["output_uns_source_genes_index"],
    min_genes_per_gp=par["min_genes_per_gp"],
@@ -4384,12 +4354,12 @@ model = NicheCompass(
    gp_sources_mask_key=par["output_varm_gp_sources_mask"],
    latent_key=par["output_obsm_embedding"],
    cat_covariates_keys=par["input_obs_covariates"],
-    cat_covariates_no_edges=par["covariates_edges"],
+    cat_covariates_no_edges=par["covariate_edges"],
    cat_covariates_embeds_keys=par["output_uns_covariate_embeddings"],
-    cat_covariates_embeds_injection_layers=par["covariate_embedding_injection_layers"],
-    gene_idx_key=par["output_uns_gene_index"],
-    target_gene_idx_key=par["output_uns_target_genes_index"],
-    source_gene_idx_key=par["output_uns_source_genes_index"],
+    cat_covariates_embeds_injection=par["covariate_embedding_injection_layers"],
+    genes_idx_key=par["output_uns_genes_index"],
+    target_genes_idx_key=par["output_uns_target_genes_index"],
+    source_genes_idx_key=par["output_uns_source_genes_index"],
    recon_adj_key=par["output_obsp_reconstructed_adj_edge_proba"],
    agg_weights_key=par["output_obsp_agg_weights"],
    include_edge_recon_loss=par["include_edge_recon_loss"],
@@ -4410,7 +4380,6 @@ model = NicheCompass(
    encoder_use_bn=par["encoder_use_bn"],
    dropout_rate_encoder=par["dropout_rate_encoder"],
    dropout_rate_graph_decoder=par["dropout_rate_graph_decoder"],
-    cat_covariates_cats=par["cat_covariates_cats"],
    n_addon_gp=par["n_addon_gp"],
    cat_covariates_embeds_nums=par["cat_covariates_embeds_nums"],
    seed=par["random_state"],
@@ -4448,7 +4417,7 @@ model.train(
 ## Save model and data
 logger.info("Saving NicheCompass model and data...")
 mdata = mu.MuData({par["modality"]: adata})
-mdata.write_h5mu(par["output"])
+mdata.write_h5mu(par["output"], compression=par["output_compression"])

 model.save(par["output_model"], save_adata=False)
 VIASHMAIN
--- a/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml
+++ b/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml
@@ -640,7 +640,7 @@ build_info:
  output: "target/nextflow/workflows/multiomics/spatial_process_samples"
  executable: "target/nextflow/workflows/multiomics/spatial_process_samples/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
  dependencies:
  - "target/dependencies/vsh/vsh/openpipeline/v3.0.0/nextflow/workflows/multiomics/process_samples"
--- a/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf
+++ b/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf
@@ -3807,7 +3807,7 @@ meta = [
    "engine" : "native",
    "output" : "/workdir/root/repo/target/nextflow/workflows/multiomics/spatial_process_samples",
    "viash_version" : "0.9.4",
-    "git_commit" : "0c1677bb93680d39ec2fb2f6bc68a2fcfae0e831",
+    "git_commit" : "9151204629228da14d7c82f49f24c607efb9251e",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/workflows/niche/nichecompass_leiden/.config.vsh.yaml
+++ b/target/nextflow/workflows/niche/nichecompass_leiden/.config.vsh.yaml
@@ -0,0 +1,816 @@
+name: "nichecompass_leiden"
+namespace: "workflows/niche"
+version: "niche-compass"
+authors:
+- name: "Dorien Roosen"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    role: "Core Team Member"
+    links:
+      email: "dorien@data-intuitive.com"
+      github: "dorien-er"
+      linkedin: "dorien-roosen"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
+- name: "Weiwei Schultz"
+  roles:
+  - "contributor"
+  info:
+    role: "Contributor"
+    organizations:
+    - name: "Janssen R&D US"
+      role: "Associate Director Data Sciences"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "string"
+    name: "--id"
+    description: "ID of the sample."
+    info: null
+    example:
+    - "foo"
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--input"
+    alternatives:
+    - "-i"
+    description: "Path to the sample."
+    info: null
+    example:
+    - "input.h5mu"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--input_gp_mask"
+    description: "JSON file containing a nested dictionary containing the gene programs,\n\
+      with keys being gene program names and values being dictionaries with keys `targets`\
+      \ and `sources`,\nwhere `targets` contains a list of the names of genes in the\
+      \ gene program for the reconstruction of the gene expression of the node itself\
+      \ (receiving node)\nand `sources` contains a list of the names of genes in the\
+      \ gene program for the reconstruction of the gene expression of the node's neighbors\
+      \ (transmitting nodes).\n"
+    info: null
+    example:
+    - "prior_knowledge_gp_mask.json"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--modality"
+    description: "Which modality to process."
+    info: null
+    default:
+    - "rna"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--layer"
+    description: "Use specified layer for calculation of qc metrics. If not specified,\
+      \ adata.X is used."
+    info: null
+    example:
+    - "raw_counts"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--input_obs_covariates"
+    description: "Keys of the adata.obs fields to use as covariates."
+    info: null
+    default:
+    - "sample_id"
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "string"
+    name: "--input_obsm_spatial_coords"
+    description: "Key in adata.obsm where spatial coordinates are stored"
+    info: null
+    default:
+    - "spatial"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Sample ID options"
+  description: "Options for adding the id to .obs on the MuData object. Having a sample\
+    \ \nid present in a requirement of several components for this pipeline.\n"
+  arguments:
+  - type: "boolean"
+    name: "--include_sample_as_covariate"
+    description: "Whether to include the sample information as a categorical covariate\
+      \ for the \nNicheCompass model.\n"
+    info: null
+    default:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--add_id_to_obs"
+    description: "Add the value passed with --id to .obs."
+    info: null
+    default:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--add_id_obs_output"
+    description: ".Obs column to add the sample IDs to. Required and only used when\
+      \ \n--add_id_to_obs is set to 'true'\n"
+    info: null
+    default:
+    - "sample_id"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--add_id_make_observation_keys_unique"
+    description: "Join the id to the .obs index (.obs_names). \nOnly used when --add_id_to_obs\
+      \ is set to 'true'.\n"
+    info: null
+    default:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Spatial Neighbors Calculation"
+  description: "Options for the calculation of the spatial neighborhood graph.\n"
+  arguments:
+  - type: "string"
+    name: "--coord_type"
+    description: "Type of coordinate system provided by `--input_obsm_spatial_coords`.\
+      \ Valid options are:\n`grid` - grid coordinates.\n`generic` - generic coordinates.\n\
+      If not provided, `grid` is used if `--input_obsm_spatial_coords` is in --input\
+      \ .uns with `--n_neighs` = 6 (Visium), otherwise `generic` is used.\n"
+    info: null
+    required: false
+    choices:
+    - "generic"
+    - "grid"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--n_spatial_neighbors"
+    description: "Depending on `--coord_type`:\n`grid` - number of neighboring tiles.\n\
+      `generic` - number of neighborhoods for non-grid data. Only used when `--delaunay\
+      \ False`.\n"
+    info: null
+    default:
+    - 6
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--delaunay"
+    description: "Whether to use Delaunay triangulation to determine spatial neighborhood\
+      \ graph.\nOnly used when `--coord_type generic`.\n"
+    info: null
+    default:
+    - false
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Gene Program Mask"
+  description: "Options for filtering gene programs based on the number of genes available\
+    \ in the data."
+  arguments:
+  - type: "integer"
+    name: "--min_genes_per_gp"
+    description: "Minimum number of genes in a gene program inluding both target and\
+      \ source genes that need to be available in the input data (gene expression\
+      \ has been probed) for a gene program not to be discarded.\n"
+    info: null
+    default:
+    - 1
+    required: false
+    min: 0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--min_source_genes_per_gp"
+    description: "Minimum number of source genes in a gene program that need to be\
+      \ available in the input data (gene expression has been probed) for a gene program\
+      \ not to be discarded.\n"
+    info: null
+    default:
+    - 0
+    required: false
+    min: 0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--min_target_genes_per_gp"
+    description: "Minimum number of target genes in a gene program that need to be\
+      \ available in the input data (gene expression has been probed) for a gene program\
+      \ not to be discarded.\n"
+    info: null
+    default:
+    - 0
+    required: false
+    min: 0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--max_genes_per_gp"
+    description: "Maximum number of genes in a gene program inluding both target and\
+      \ source genes that can be available in the input data (gene expression has\
+      \ been probed) for a gene program not to be discarded.\n"
+    info: null
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--max_source_genes_per_gp"
+    description: "Maximum number of source genes in a gene program that can be available\
+      \ in the input data (gene expression has been probed) for a gene program not\
+      \ to be discarded.\n"
+    info: null
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--max_target_genes_per_gp"
+    description: "Maximum number of target genes in a gene program that can be available\
+      \ in the input data (gene expression has been probed) for a gene program not\
+      \ to be discarded.\n"
+    info: null
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--filter_genes_not_in_masks"
+    description: "Whether to remove the genes that are not in the gp masks from the\
+      \ input data.\n"
+    info: null
+    direction: "input"
+- name: "NicheCompass Model Architecture"
+  description: "Options for the NicheCompass model architecture."
+  arguments:
+  - type: "boolean"
+    name: "--covariate_edges"
+    description: "List of booleans that indicate whether there can be edges between\
+      \ different categories of the categorical covariates.\nIf this is `True` for\
+      \ a specific categorical covariate, this covariate will be excluded from the\
+      \ edge reconstruction loss.\nNeeds to match the length and order of `--input_obs_covariates`.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "string"
+    name: "--gene_expr_recon_dist"
+    description: "The distribution used for gene expression reconstruction. \nIf `nb`,\
+      \ uses a negative binomial distribution. \nIf `zinb`, uses a zero-inflated negative\
+      \ binomial distribution.\n"
+    info: null
+    default:
+    - "nb"
+    required: false
+    choices:
+    - "nb"
+    - "zinb"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--log_variational"
+    description: "Whether to transform x by log(x+1) prior to encoding for numerical\
+      \ stability (not for normalization).\n"
+    info: null
+    default:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--node_label_method"
+    description: "Node label method that will be used for omics reconstruction.\n\
+      If `one-hop-sum`, uses a concatenation of the node's input features with the\
+      \ sum of the input features of all nodes in the node's one-hop neighborhood.\n\
+      If `one-hop-norm`, uses a concatenation of the node's input features with the\
+      \ node's one-hop neighbors input features normalized as per Kipf, T. N. & Welling,\
+      \ M. Semi-Supervised Classification with Graph Convolutional Networks. arXiv\
+      \ [cs.LG] (2016).\nIf `one-hop-attention`, uses a concatenation of the node's\
+      \ input features with the node's one-hop neighbors input features weighted by\
+      \ an attention mechanism.\n"
+    info: null
+    default:
+    - "one-hop-norm"
+    required: false
+    choices:
+    - "one-hop-norm"
+    - "two-hop-norm"
+    - "one-hop-attention"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--active_gp_thresh_ratio"
+    description: "Ratio that determines which gene programs are considered active\
+      \ and are used in the latent representation after model training.\nAll inactive\
+      \ gene programs will be dropped during model training after a determined number\
+      \ of epochs.\nAggregations of the absolute values of the gene weights of the\
+      \ gene expression decoder per gene program are calculated.\nThe maximum value,\
+      \ i.e. the value of the gene program with the highest aggregated value will\
+      \ be used as a benchmark and all gene programs whose aggregated value is smaller\
+      \ than `--active_gp_thresh_ratio` times this maximum value will be set to inactive.\n\
+      If set to 0, all gene programs will be considered active.\n"
+    info: null
+    default:
+    - 0.1
+    required: false
+    min: 0.0
+    max: 1.0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--active_gp_type"
+    description: "Type to determine active gene programs. \nCan be `mixed`, in which\
+      \ case active gene programs are determined across prior and add-on gene programs\
+      \ jointly,\nor `separate` in which case they are determined separately for prior\
+      \ and add-on gene programs.\n"
+    info: null
+    default:
+    - "separate"
+    required: false
+    choices:
+    - "mixed"
+    - "separate"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--n_addon_gp"
+    description: "Number of addon gene programs (i.e. gene programs that are not included\
+      \ in masks but can be learned de novo).\n"
+    info: null
+    default:
+    - 100
+    required: false
+    min: 0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--cat_covariates_embeds_nums"
+    description: "Number of embedding nodes for all categorical covariates.\nMust\
+      \ be the same length as `--input_obs_covariates`.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--random_state"
+    description: "Random seed for reproducibility.\n"
+    info: null
+    default:
+    - 0
+    required: false
+    min: 0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "NicheCompass Training Parameters"
+  description: "Options for training the NicheCompass model."
+  arguments:
+  - type: "integer"
+    name: "--n_epochs"
+    description: "Number of training epochs"
+    info: null
+    default:
+    - 100
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--n_epochs_all_gps"
+    description: "Number of epochs during which all gene programs are used for model\
+      \ training.\nAfter that only active gene programs are retained.\n"
+    info: null
+    default:
+    - 25
+    required: false
+    min: 0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--n_epochs_no_edge_recon"
+    description: "Number of epochs during which the edge reconstruction loss is excluded\
+      \ from backpropagation for pretraining using the other loss components.\n"
+    info: null
+    default:
+    - 0
+    required: false
+    min: 0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--n_epochs_no_cat_covariates_contrastive"
+    description: "Number of epochs during which the categorical covariates contrastive\
+      \ loss is excluded from backpropagation for pretraining using the other loss\
+      \ components.\n"
+    info: null
+    default:
+    - 5
+    required: false
+    min: 0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--lr"
+    description: "Learning rate"
+    info: null
+    default:
+    - 0.001
+    required: false
+    min: 0.0
+    max: 1.0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--weight_decay"
+    description: "Weight decay (L2 penalty)."
+    info: null
+    default:
+    - 0.001
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--edge_val_ratio"
+    description: "Fraction of the data that is used as validation set on edge-level.\
+      \ The rest of the data will be used as training set on edge-level.\n"
+    info: null
+    default:
+    - 0.1
+    required: false
+    min: 0.0
+    max: 1.0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--node_val_ratio"
+    description: "Fraction of the data that is used as validation set on node-level.\
+      \ The rest of the data will be used as training set on node-level.\n"
+    info: null
+    default:
+    - 0.1
+    required: false
+    min: 0.0
+    max: 1.0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--edge_batch_size"
+    description: "Batch size for the edge-level dataloaders.\n"
+    info: null
+    default:
+    - 256
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--node_batch_size"
+    description: "Batch size for the node-level dataloaders.\nIf not provided, is\
+      \ automatically determined based on `--edge_batch_size`.\n"
+    info: null
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--n_sampled_neighbors"
+    description: "Number of neighbors that are sampled during model training from\
+      \ the spatial neighborhood graph.\nIf set to -1, all direct neighbors are included.\n"
+    info: null
+    default:
+    - -1
+    required: false
+    min: -1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Clustering options"
+  arguments:
+  - type: "string"
+    name: "--obs_cluster"
+    description: "Prefix for the .obs keys under which to add the cluster labels.\
+      \ Newly created columns in .obs will \nbe created from the specified value for\
+      \ '--obs_cluster' suffixed with an underscore and one of the resolutions\nresolutions\
+      \ specified in '--leiden_resolution'.\n"
+    info: null
+    default:
+    - "nichecompass_leiden"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--leiden_resolution"
+    description: "Control the coarseness of the clustering. Higher values lead to\
+      \ more clusters."
+    info: null
+    default:
+    - 1.0
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+- name: "Umap options"
+  arguments:
+  - type: "string"
+    name: "--obsm_umap"
+    description: "In which .obsm slot to store the resulting UMAP embedding."
+    info: null
+    default:
+    - "X_leiden_nichecompass_umap"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Neighbour calculation"
+  arguments:
+  - type: "string"
+    name: "--uns_neighbors"
+    description: "In which .uns slot to store various neighbor output objects."
+    info: null
+    default:
+    - "nichecompass_neighbors"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--obsp_neighbor_distances"
+    description: "In which .obsp slot to store the distance matrix between the resulting\
+      \ neighbors."
+    info: null
+    default:
+    - "nichecompass_distances"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--obsp_neighbor_connectivities"
+    description: "In which .obsp slot to store the connectivities matrix between the\
+      \ resulting neighbors."
+    info: null
+    default:
+    - "nichecompass_connectivities"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "Destination path to the output."
+    info: null
+    example:
+    - "output.h5mu"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_model"
+    description: "Directory to save the trained NicheCompass model."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--output_obsm_embedding"
+    description: "Key of the obsm field where the latent / gene program representation\
+      \ of active gene programs will be stored after NicheCompass model training.\n"
+    info: null
+    default:
+    - "nichecompass_latent"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "nextflow_script"
+  path: "main.nf"
+  is_executable: true
+  entrypoint: "run_wf"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
+description: "A pipeline to compute the spatial neighborhood graph, perform nichecompass\
+  \ embedding followed by Leiden clustering."
+test_resources:
+- type: "nextflow_script"
+  path: "test.nf"
+  is_executable: true
+  entrypoint: "test_wf"
+- type: "file"
+  path: "xenium_tiny.h5mu"
+- type: "file"
+  path: "Lung5_Rep2_tiny.h5mu"
+- type: "file"
+  path: "prior_knowledge_gp_mask.json"
+info:
+  test_dependencies:
+  - name: "nichecompass_leiden_test"
+    namespace: "test_workflows/niche"
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+dependencies:
+- name: "dataflow/obsp_block_concatenation"
+  repository:
+    type: "local"
+- name: "neighbors/spatial_neighborhood_graph"
+  repository:
+    type: "local"
+- name: "nichecompass/nichecompass"
+  repository:
+    type: "local"
+- name: "metadata/add_id"
+  repository:
+    type: "vsh"
+    repo: "openpipeline"
+    tag: "v3.0.0"
+- name: "workflows/multiomics/neighbors_leiden_umap"
+  repository:
+    type: "vsh"
+    repo: "openpipeline"
+    tag: "v3.0.0"
+repositories:
+- type: "vsh"
+  name: "openpipeline"
+  repo: "openpipeline"
+  tag: "v3.0.0"
+links:
+  repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
+  docker_registry: "ghcr.io"
+runners:
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
+  debug: false
+  container: "docker"
+engines:
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/workflows/niche/nichecompass_leiden/config.vsh.yaml"
+  runner: "nextflow"
+  engine: "native"
+  output: "target/nextflow/workflows/niche/nichecompass_leiden"
+  executable: "target/nextflow/workflows/niche/nichecompass_leiden/main.nf"
+  viash_version: "0.9.4"
+  git_commit: "9151204629228da14d7c82f49f24c607efb9251e"
+  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
+  dependencies:
+  - "target/nextflow/dataflow/obsp_block_concatenation"
+  - "target/nextflow/neighbors/spatial_neighborhood_graph"
+  - "target/nextflow/nichecompass/nichecompass"
+  - "target/dependencies/vsh/vsh/openpipeline/v3.0.0/nextflow/metadata/add_id"
+  - "target/dependencies/vsh/vsh/openpipeline/v3.0.0/nextflow/workflows/multiomics/neighbors_leiden_umap"
+package_config:
+  name: "openpipeline_spatial"
+  version: "niche-compass"
+  info:
+    test_resources:
+    - type: "s3"
+      path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
+      dest: "resources_test"
+  repositories:
+  - type: "vsh"
+    name: "openpipeline"
+    repo: "openpipeline"
+    tag: "v3.0.0"
+  viash_version: "0.9.4"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
+    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    )'"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'niche-compass'"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
+    docker_registry: "ghcr.io"
--- a/target/nextflow/workflows/niche/nichecompass_leiden/main.nf
+++ b/target/nextflow/workflows/niche/nichecompass_leiden/main.nf
--- a/Show More
+++ b/Show More