Build branch build/main with version build_main (33c1a3a)

Build pipeline: openpipelines-bio.openpipeline-spatial.build-main-rtgd7 Source commit: 33c1a3afb0 Source message: deploy: a14a97d04951b3cd02cf6a5dff6ee4c539b3aae8
2025-08-19 12:22:13 +00:00
parent b1ffb24eb9
commit a606f73474
47 changed files with 6485 additions and 40 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,7 +8,7 @@

 * `mapping/spaceranger_count`: Added a spaceranger count component (PR #2).

-* `convert/from_spatialdata_to_h5mu`, `convert/from_xenium_to_spatialdata`: Added converter components for xenium data (PR #1).
+* `convert/from_spatialdata_to_h5mu`, `convert/from_xenium_to_spatialdata`, `convert/from_xenium_to_h5mu`: Added converter components for xenium data (PR #1, #10).

 * `convert/from_xenium_to_spatialexperiment`, `convert/from_cosmx_to_spatialexperiment`: Added converter components for Xenium or CosMx data to SpatialExperiment objects (PR #9).

--- a/src/base/h5_compression_argument.yaml
+++ b/src/base/h5_compression_argument.yaml
@@ -0,0 +1,9 @@
+arguments:
+  - name: "--output_compression"
+    description: |
+      Compression format to use for the output AnnData and/or Mudata objects.
+      By default no compression is applied.
+    type: string
+    choices: ["gzip", "lzf"]
+    required: false
+    example: "gzip"
--- a/src/convert/from_xenium_to_h5mu/config.vsh.yaml
+++ b/src/convert/from_xenium_to_h5mu/config.vsh.yaml
@@ -0,0 +1,69 @@
+name: "from_xenium_to_h5mu"
+namespace: "convert"
+scope: "public"
+description: |
+  Converts the output from Xenium to a single .h5mu file, where the count matrix is written to the `rna` modality.
+  The following files are expected to be present in the Xenium output bundle:
+  ├── cell_feature_matrix.h5
+  ├── cells.parquet
+  ├── experiment.xenium
+  └── metrics_summary.csv
+
+authors:
+  - __merge__: /src/authors/dorien_roosen.yaml
+    roles: [ maintainer ]
+arguments:
+  - name: "--input"
+    alternatives: ["-i"]
+    type: file
+    description: Input folder. Must contain the output from a Xenium run.
+    example: xenium_output_bundle
+    direction: input
+    required: true
+  - name: "--output"
+    alternatives: ["-o"]
+    type: file
+    description: Output .h5mu file.
+    example: "xenium.h5mu"
+    direction: output
+  - name: "--obsm_coordinates"
+    type: string
+    description: Name of the .obsm slot under which to store the cell centroid coordinates.
+    default: "spatial"
+  - name: "--uns_experiment"
+    type: string
+    description: Name of the .uns slot under which to store the Xenium experiment specifications.
+    default: "xenium_experiment"
+  - name: "--uns_metrics"
+    type: string
+    description: Name of the .uns slot under which to store the summary QC metrics.
+    default: "xenium_metrics"
+__merge__: [., /src/base/h5_compression_argument.yaml]
+
+resources:
+  - type: python_script
+    path: script.py
+  - path: /src/utils/setup_logger.py
+test_resources:
+  - type: python_script
+    path: test.py
+  - path: /resources_test/xenium/xenium_tiny
+engines:
+  - type: docker
+    image: python:3.12-slim
+    setup:
+      - type: apt
+        packages: 
+          - procps
+      - type: python
+        __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/scanpy.yaml, .]
+        packages:
+          - pyarrow
+    test_setup:
+      - type: python
+        __merge__: [ /src/base/requirements/viashpy.yaml, .]
+runners:
+  - type: executable
+  - type: nextflow
+    directives:
+      label: [lowmem, singlecpu]
--- a/src/convert/from_xenium_to_h5mu/script.py
+++ b/src/convert/from_xenium_to_h5mu/script.py
@@ -0,0 +1,75 @@
+import sys
+from pathlib import Path
+import scanpy as sc
+import pandas as pd
+import mudata as mu
+import json
+
+## VIASH START
+par = {
+    "input": "./resources_test/xenium/xenium_tiny",
+    "output": "xenium_tiny_test.h5mu",
+    "output_compression": "gzip",
+    "obsm_coordinates": "spatial",
+    "uns_experiment": "xenium_experiment",
+    "uns_metrics": "xenium_metrics",
+}
+meta = {"resources_dir": "src/utils"}
+## VIASH END
+
+sys.path.append(meta["resources_dir"])
+from setup_logger import setup_logger
+
+logger = setup_logger()
+
+# Expected folder structure (showing only relevant files):
+# ├── cell_feature_matrix.h5
+# ├── cells.parquet
+# ├── experiment.xenium
+# └── metrics_summary.csv
+input_dir = Path(par["input"])
+input_data = {
+    "count_matrix": input_dir / "cell_feature_matrix.h5",
+    "cells_metadata": input_dir / "cells.parquet",
+    "experiment": input_dir / "experiment.xenium",
+    "metrics_summary": input_dir / "metrics_summary.csv",
+}
+
+
+def _format_cell_id_column(cell_id_column: pd.Series) -> pd.Series:
+    """Convert cell IDs to string format, decoding bytes if necessary."""
+    return cell_id_column.apply(
+        lambda x: x.decode("utf-8") if isinstance(x, bytes) else str(x)
+    )
+
+
+# Read data from Xenium output bundle
+logger.info("Reading input data...")
+
+assert all([file.exists() for file in input_data.values()]), (
+    f"Not all required input files are found. Make sure that {par['input']} contains {input_data.values()}."
+)
+
+adata = sc.read_10x_h5(input_data["count_matrix"])
+metadata = pd.read_parquet(input_data["cells_metadata"], engine="pyarrow")
+with open(input_data["experiment"], "r") as f:
+    specs = json.load(f)
+metrics_summary = pd.read_csv(
+    input_data["metrics_summary"], decimal=".", quotechar='"', thousands=","
+)
+
+# Extract and format required columns
+cell_ids = _format_cell_id_column(metadata["cell_id"])
+coordinates = metadata[["x_centroid", "y_centroid"]].to_numpy()
+metadata.drop(["cell_id", "x_centroid", "y_centroid"], axis=1, inplace=True)
+
+# Updata AnnData with metadata
+adata.obs = metadata
+adata.obs_names = cell_ids
+adata.obsm[par["obsm_coordinates"]] = coordinates
+adata.uns[par["uns_experiment"]] = specs
+adata.uns[par["uns_metrics"]] = metrics_summary
+
+# Write output MuData
+mdata = mu.MuData({"rna": adata})
+mdata.write_h5mu(par["output"], compression=par["output_compression"])
--- a/src/convert/from_xenium_to_h5mu/test.py
+++ b/src/convert/from_xenium_to_h5mu/test.py
@@ -0,0 +1,97 @@
+import pytest
+import sys
+import mudata as mu
+
+## VIASH START
+meta = {
+    "executable": "./target/executable/convert/from_cellranger_multi_to_h5mu/from_cellranger_multi_to_h5mu",
+    "resources_dir": "resources_test/",
+    "config": "src/convert/from_cellranger_multi_to_h5mu/config.vsh.yaml",
+}
+## VIASH END
+
+input = f"{meta['resources_dir']}/xenium_tiny"
+
+
+def test_simple_execution(run_component, tmp_path):
+    output = tmp_path / "xenium.h5mu"
+
+    # run component
+    run_component(
+        ["--input", input, "--output", str(output), "--output_compression", "gzip"]
+    )
+
+    assert output.is_file(), "output file was not created"
+
+    mdata = mu.read_h5mu(output)
+    assert list(mdata.mod.keys()) == ["rna"], "Expected modality rna"
+    adata = mdata.mod["rna"]
+
+    assert list(adata.obs.keys()) == [
+        "transcript_counts",
+        "control_probe_counts",
+        "genomic_control_counts",
+        "control_codeword_counts",
+        "unassigned_codeword_counts",
+        "deprecated_codeword_counts",
+        "total_counts",
+        "cell_area",
+        "nucleus_area",
+        "nucleus_count",
+        "segmentation_method",
+    ]
+
+    assert list(adata.uns.keys()) == ["xenium_experiment", "xenium_metrics"]
+    assert list(adata.obsm.keys()) == ["spatial"]
+    assert list(adata.var.keys()) == ["gene_ids", "feature_types", "genome"]
+
+    assert adata.X.dtype.kind == "f"
+    assert all(adata.var["feature_types"] == "Gene Expression")
+    assert adata.obsm["spatial"].dtype == "float"
+    obs_counts = [
+        "transcript_counts",
+        "control_probe_counts",
+        "genomic_control_counts",
+        "unassigned_codeword_counts",
+        "deprecated_codeword_counts",
+        "total_counts",
+        "nucleus_count",
+    ]
+    assert all([adata.obs[obs].dtype == "int" for obs in obs_counts])
+    obs_areas = ["cell_area", "nucleus_area"]
+    assert all([adata.obs[obs].dtype == "float" for obs in obs_areas])
+
+
+def test_rename_fields(run_component, tmp_path):
+    output = tmp_path / "xenium.h5mu"
+
+    # run component
+    run_component(
+        [
+            "--input",
+            input,
+            "--output",
+            str(output),
+            "--obsm_coordinates",
+            "test_coord",
+            "--uns_experiment",
+            "test_experiment",
+            "--uns_metrics",
+            "test_metrics",
+            "--output_compression",
+            "gzip",
+        ]
+    )
+
+    assert output.is_file(), "output file was not created"
+
+    mdata = mu.read_h5mu(output)
+    assert list(mdata.mod.keys()) == ["rna"]
+    adata = mdata.mod["rna"]
+
+    assert list(adata.uns.keys()) == ["test_experiment", "test_metrics"]
+    assert list(adata.obsm.keys()) == ["test_coord"]
+
+
+if __name__ == "__main__":
+    sys.exit(pytest.main([__file__]))
--- a/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml
@@ -229,7 +229,7 @@ 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: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
+  git_commit: "33c1a3afb0dfebceff25b0a0104bf16582611716"
  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
@@ -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_cosmx_to_h5mu"
-LABEL org.opencontainers.image.created="2025-08-18T07:54:17Z"
+LABEL org.opencontainers.image.created="2025-08-19T11:57:43Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="226d7de695d56f116dd1ba8e08a51ebf63b153b3"
+LABEL org.opencontainers.image.revision="33c1a3afb0dfebceff25b0a0104bf16582611716"
 LABEL org.opencontainers.image.version="build_main"

 VIASHDOCKER
--- a/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml
+++ b/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml
@@ -236,7 +236,7 @@ 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: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
+  git_commit: "33c1a3afb0dfebceff25b0a0104bf16582611716"
  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="2025-08-18T07:54:16Z"
+LABEL org.opencontainers.image.created="2025-08-19T11:57:42Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="226d7de695d56f116dd1ba8e08a51ebf63b153b3"
+LABEL org.opencontainers.image.revision="33c1a3afb0dfebceff25b0a0104bf16582611716"
 LABEL org.opencontainers.image.version="build_main"

 VIASHDOCKER
--- a/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
@@ -224,7 +224,7 @@ 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: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
+  git_commit: "33c1a3afb0dfebceff25b0a0104bf16582611716"
  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="2025-08-18T07:54:16Z"
+LABEL org.opencontainers.image.created="2025-08-19T11:57:42Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="226d7de695d56f116dd1ba8e08a51ebf63b153b3"
+LABEL org.opencontainers.image.revision="33c1a3afb0dfebceff25b0a0104bf16582611716"
 LABEL org.opencontainers.image.version="build_main"

 VIASHDOCKER
--- a/target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml
@@ -0,0 +1,272 @@
+name: "from_xenium_to_h5mu"
+namespace: "convert"
+version: "build_main"
+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: "Arguments"
+  arguments:
+  - type: "file"
+    name: "--input"
+    alternatives:
+    - "-i"
+    description: "Input folder. Must contain the output from a Xenium run."
+    info: null
+    example:
+    - "xenium_output_bundle"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output"
+    alternatives:
+    - "-o"
+    description: "Output .h5mu file."
+    info: null
+    example:
+    - "xenium.h5mu"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--obsm_coordinates"
+    description: "Name of the .obsm slot under which to store the cell centroid coordinates."
+    info: null
+    default:
+    - "spatial"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--uns_experiment"
+    description: "Name of the .uns slot under which to store the Xenium experiment\
+      \ specifications."
+    info: null
+    default:
+    - "xenium_experiment"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--uns_metrics"
+    description: "Name of the .uns slot under which to store the summary QC metrics."
+    info: null
+    default:
+    - "xenium_metrics"
+    required: false
+    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"
+  is_executable: true
+- type: "file"
+  path: "setup_logger.py"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
+description: "Converts the output from Xenium to a single .h5mu file, where the count\
+  \ matrix is written to the `rna` modality.\nThe following files are expected to\
+  \ be present in the Xenium output bundle:\n├── cell_feature_matrix.h5\n├── cells.parquet\n\
+  ├── experiment.xenium\n└── metrics_summary.csv\n"
+test_resources:
+- type: "python_script"
+  path: "test.py"
+  is_executable: true
+- type: "file"
+  path: "xenium_tiny"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+repositories:
+- type: "github"
+  name: "openpipeline"
+  repo: "openpipelines-bio/openpipeline"
+  tag: "2.1.2"
+- type: "vsh"
+  name: "openpipeline_incubator"
+  repo: "openpipeline_incubator"
+  tag: "build/main"
+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:
+    - "lowmem"
+    - "singlecpu"
+    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: "build_main"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "procps"
+    interactive: false
+  - type: "python"
+    user: false
+    packages:
+    - "anndata~=0.11.1"
+    - "mudata~=0.3.1"
+    - "scanpy~=1.10.4"
+    - "pyarrow"
+    script:
+    - "exec(\"try:\\n  import awkward\\nexcept ModuleNotFoundError:\\n  exit(0)\\\
+      nelse:  exit(1)\")"
+    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/convert/from_xenium_to_h5mu/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  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: "33c1a3afb0dfebceff25b0a0104bf16582611716"
+  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
+package_config:
+  name: "openpipeline_spatial"
+  version: "build_main"
+  info:
+    test_resources:
+    - type: "s3"
+      path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
+      dest: "resources_test"
+  repositories:
+  - type: "github"
+    name: "openpipeline"
+    repo: "openpipelines-bio/openpipeline"
+    tag: "2.1.2"
+  - type: "vsh"
+    name: "openpipeline_incubator"
+    repo: "openpipeline_incubator"
+    tag: "build/main"
+  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 := 'build_main'"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
+    docker_registry: "ghcr.io"
--- a/target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu
+++ b/target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu
--- a/target/executable/convert/from_xenium_to_h5mu/nextflow_labels.config
+++ b/target/executable/convert/from_xenium_to_h5mu/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/convert/from_xenium_to_h5mu/setup_logger.py
+++ b/target/executable/convert/from_xenium_to_h5mu/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/convert/from_xenium_to_spatialdata/.config.vsh.yaml
+++ b/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml
@@ -318,7 +318,7 @@ 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: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
+  git_commit: "33c1a3afb0dfebceff25b0a0104bf16582611716"
  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
@@ -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 convert from_xenium_to_spatialdata"
-LABEL org.opencontainers.image.created="2025-08-18T07:54:17Z"
+LABEL org.opencontainers.image.created="2025-08-19T11:57:43Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="226d7de695d56f116dd1ba8e08a51ebf63b153b3"
+LABEL org.opencontainers.image.revision="33c1a3afb0dfebceff25b0a0104bf16582611716"
 LABEL org.opencontainers.image.version="build_main"

 VIASHDOCKER
--- a/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml
+++ b/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml
@@ -226,7 +226,7 @@ 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: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
+  git_commit: "33c1a3afb0dfebceff25b0a0104bf16582611716"
  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="2025-08-18T07:54:16Z"
+LABEL org.opencontainers.image.created="2025-08-19T11:57:42Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="226d7de695d56f116dd1ba8e08a51ebf63b153b3"
+LABEL org.opencontainers.image.revision="33c1a3afb0dfebceff25b0a0104bf16582611716"
 LABEL org.opencontainers.image.version="build_main"

 VIASHDOCKER
--- a/target/executable/filter/subset_cosmx/.config.vsh.yaml
+++ b/target/executable/filter/subset_cosmx/.config.vsh.yaml
@@ -231,7 +231,7 @@ build_info:
  output: "target/executable/filter/subset_cosmx"
  executable: "target/executable/filter/subset_cosmx/subset_cosmx"
  viash_version: "0.9.4"
-  git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
+  git_commit: "33c1a3afb0dfebceff25b0a0104bf16582611716"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/executable/filter/subset_cosmx/subset_cosmx
+++ b/target/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="2025-08-18T07:54:16Z"
+LABEL org.opencontainers.image.created="2025-08-19T11:57:42Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="226d7de695d56f116dd1ba8e08a51ebf63b153b3"
+LABEL org.opencontainers.image.revision="33c1a3afb0dfebceff25b0a0104bf16582611716"
 LABEL org.opencontainers.image.version="build_main"

 VIASHDOCKER
--- a/target/executable/mapping/spaceranger_count/.config.vsh.yaml
+++ b/target/executable/mapping/spaceranger_count/.config.vsh.yaml
@@ -430,7 +430,7 @@ build_info:
  output: "target/executable/mapping/spaceranger_count"
  executable: "target/executable/mapping/spaceranger_count/spaceranger_count"
  viash_version: "0.9.4"
-  git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
+  git_commit: "33c1a3afb0dfebceff25b0a0104bf16582611716"
  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="2025-08-18T07:54:17Z"
+LABEL org.opencontainers.image.created="2025-08-19T11:57:43Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="226d7de695d56f116dd1ba8e08a51ebf63b153b3"
+LABEL org.opencontainers.image.revision="33c1a3afb0dfebceff25b0a0104bf16582611716"
 LABEL org.opencontainers.image.version="build_main"

 VIASHDOCKER
--- a/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml
@@ -229,7 +229,7 @@ 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: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
+  git_commit: "33c1a3afb0dfebceff25b0a0104bf16582611716"
  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
@@ -3337,7 +3337,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_h5mu",
    "viash_version" : "0.9.4",
-    "git_commit" : "226d7de695d56f116dd1ba8e08a51ebf63b153b3",
+    "git_commit" : "33c1a3afb0dfebceff25b0a0104bf16582611716",
    "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
@@ -236,7 +236,7 @@ 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: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
+  git_commit: "33c1a3afb0dfebceff25b0a0104bf16582611716"
  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
@@ -3328,7 +3328,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_spatialexperiment",
    "viash_version" : "0.9.4",
-    "git_commit" : "226d7de695d56f116dd1ba8e08a51ebf63b153b3",
+    "git_commit" : "33c1a3afb0dfebceff25b0a0104bf16582611716",
    "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
@@ -224,7 +224,7 @@ 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: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
+  git_commit: "33c1a3afb0dfebceff25b0a0104bf16582611716"
  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
@@ -3336,7 +3336,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_spatialdata_to_h5mu",
    "viash_version" : "0.9.4",
-    "git_commit" : "226d7de695d56f116dd1ba8e08a51ebf63b153b3",
+    "git_commit" : "33c1a3afb0dfebceff25b0a0104bf16582611716",
    "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
@@ -0,0 +1,272 @@
+name: "from_xenium_to_h5mu"
+namespace: "convert"
+version: "build_main"
+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: "Arguments"
+  arguments:
+  - type: "file"
+    name: "--input"
+    alternatives:
+    - "-i"
+    description: "Input folder. Must contain the output from a Xenium run."
+    info: null
+    example:
+    - "xenium_output_bundle"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output"
+    alternatives:
+    - "-o"
+    description: "Output .h5mu file."
+    info: null
+    example:
+    - "xenium.h5mu"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--obsm_coordinates"
+    description: "Name of the .obsm slot under which to store the cell centroid coordinates."
+    info: null
+    default:
+    - "spatial"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--uns_experiment"
+    description: "Name of the .uns slot under which to store the Xenium experiment\
+      \ specifications."
+    info: null
+    default:
+    - "xenium_experiment"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--uns_metrics"
+    description: "Name of the .uns slot under which to store the summary QC metrics."
+    info: null
+    default:
+    - "xenium_metrics"
+    required: false
+    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"
+  is_executable: true
+- type: "file"
+  path: "setup_logger.py"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
+description: "Converts the output from Xenium to a single .h5mu file, where the count\
+  \ matrix is written to the `rna` modality.\nThe following files are expected to\
+  \ be present in the Xenium output bundle:\n├── cell_feature_matrix.h5\n├── cells.parquet\n\
+  ├── experiment.xenium\n└── metrics_summary.csv\n"
+test_resources:
+- type: "python_script"
+  path: "test.py"
+  is_executable: true
+- type: "file"
+  path: "xenium_tiny"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+repositories:
+- type: "github"
+  name: "openpipeline"
+  repo: "openpipelines-bio/openpipeline"
+  tag: "2.1.2"
+- type: "vsh"
+  name: "openpipeline_incubator"
+  repo: "openpipeline_incubator"
+  tag: "build/main"
+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:
+    - "lowmem"
+    - "singlecpu"
+    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: "build_main"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "procps"
+    interactive: false
+  - type: "python"
+    user: false
+    packages:
+    - "anndata~=0.11.1"
+    - "mudata~=0.3.1"
+    - "scanpy~=1.10.4"
+    - "pyarrow"
+    script:
+    - "exec(\"try:\\n  import awkward\\nexcept ModuleNotFoundError:\\n  exit(0)\\\
+      nelse:  exit(1)\")"
+    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/convert/from_xenium_to_h5mu/config.vsh.yaml"
+  runner: "nextflow"
+  engine: "docker|native"
+  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: "33c1a3afb0dfebceff25b0a0104bf16582611716"
+  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
+package_config:
+  name: "openpipeline_spatial"
+  version: "build_main"
+  info:
+    test_resources:
+    - type: "s3"
+      path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
+      dest: "resources_test"
+  repositories:
+  - type: "github"
+    name: "openpipeline"
+    repo: "openpipelines-bio/openpipeline"
+    tag: "2.1.2"
+  - type: "vsh"
+    name: "openpipeline_incubator"
+    repo: "openpipeline_incubator"
+    tag: "build/main"
+  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 := 'build_main'"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
+    docker_registry: "ghcr.io"
--- a/target/nextflow/convert/from_xenium_to_h5mu/main.nf
+++ b/target/nextflow/convert/from_xenium_to_h5mu/main.nf
--- a/target/nextflow/convert/from_xenium_to_h5mu/nextflow.config
+++ b/target/nextflow/convert/from_xenium_to_h5mu/nextflow.config
@@ -0,0 +1,126 @@
+manifest {
+  name = 'convert/from_xenium_to_h5mu'
+  mainScript = 'main.nf'
+  nextflowVersion = '!>=20.12.1-edge'
+  version = 'build_main'
+  description = 'Converts the output from Xenium to a single .h5mu file, where the count matrix is written to the `rna` modality.\nThe following files are expected to be present in the Xenium output bundle:\n├── cell_feature_matrix.h5\n├── cells.parquet\n├── experiment.xenium\n└── metrics_summary.csv\n'
+  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/convert/from_xenium_to_h5mu/nextflow_labels.config
+++ b/target/nextflow/convert/from_xenium_to_h5mu/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 '${process.maxRetries}' are valid!"
+        System.exit(1)
+  }
+}
--- a/target/nextflow/convert/from_xenium_to_h5mu/nextflow_schema.json
+++ b/target/nextflow/convert/from_xenium_to_h5mu/nextflow_schema.json
@@ -0,0 +1,76 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "title": "from_xenium_to_h5mu",
+  "description": "Converts the output from Xenium to a single .h5mu file, where the count matrix is written to the `rna` modality.\nThe following files are expected to be present in the Xenium output bundle:\n├── cell_feature_matrix.h5\n├── cells.parquet\n├── experiment.xenium\n└── metrics_summary.csv\n",
+  "type": "object",
+  "$defs": {
+    "arguments": {
+      "title": "Arguments",
+      "type": "object",
+      "description": "No description",
+      "properties": {
+        "input": {
+          "type": "string",
+          "format": "path",
+          "exists": true,
+          "description": "Input folder",
+          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"xenium_output_bundle\"`. "
+        },
+        "output": {
+          "type": "string",
+          "format": "path",
+          "description": "Output .h5mu file.",
+          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output.h5mu\"`, direction: `output`, example: `\"xenium.h5mu\"`. ",
+          "default": "$id.$key.output.h5mu"
+        },
+        "obsm_coordinates": {
+          "type": "string",
+          "description": "Name of the .obsm slot under which to store the cell centroid coordinates.",
+          "help_text": "Type: `string`, multiple: `False`, default: `\"spatial\"`. ",
+          "default": "spatial"
+        },
+        "uns_experiment": {
+          "type": "string",
+          "description": "Name of the .uns slot under which to store the Xenium experiment specifications.",
+          "help_text": "Type: `string`, multiple: `False`, default: `\"xenium_experiment\"`. ",
+          "default": "xenium_experiment"
+        },
+        "uns_metrics": {
+          "type": "string",
+          "description": "Name of the .uns slot under which to store the summary QC metrics.",
+          "help_text": "Type: `string`, multiple: `False`, default: `\"xenium_metrics\"`. ",
+          "default": "xenium_metrics"
+        },
+        "output_compression": {
+          "type": "string",
+          "description": "Compression format to use for the output AnnData and/or Mudata objects.\nBy default no compression is applied.\n",
+          "help_text": "Type: `string`, multiple: `False`, example: `\"gzip\"`, choices: ``gzip`, `lzf``. ",
+          "enum": [
+            "gzip",
+            "lzf"
+          ]
+        }
+      }
+    },
+    "nextflow input-output arguments": {
+      "title": "Nextflow input-output arguments",
+      "type": "object",
+      "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
+      "properties": {
+        "publish_dir": {
+          "type": "string",
+          "description": "Path to an output directory.",
+          "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
+        }
+      }
+    }
+  },
+  "allOf": [
+    {
+      "$ref": "#/$defs/arguments"
+    },
+    {
+      "$ref": "#/$defs/nextflow input-output arguments"
+    }
+  ]
+}
--- a/target/nextflow/convert/from_xenium_to_h5mu/setup_logger.py
+++ b/target/nextflow/convert/from_xenium_to_h5mu/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/convert/from_xenium_to_spatialdata/.config.vsh.yaml
+++ b/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml
@@ -318,7 +318,7 @@ 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: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
+  git_commit: "33c1a3afb0dfebceff25b0a0104bf16582611716"
  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
@@ -3431,7 +3431,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialdata",
    "viash_version" : "0.9.4",
-    "git_commit" : "226d7de695d56f116dd1ba8e08a51ebf63b153b3",
+    "git_commit" : "33c1a3afb0dfebceff25b0a0104bf16582611716",
    "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
@@ -226,7 +226,7 @@ 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: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
+  git_commit: "33c1a3afb0dfebceff25b0a0104bf16582611716"
  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
@@ -3317,7 +3317,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialexperiment",
    "viash_version" : "0.9.4",
-    "git_commit" : "226d7de695d56f116dd1ba8e08a51ebf63b153b3",
+    "git_commit" : "33c1a3afb0dfebceff25b0a0104bf16582611716",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/filter/subset_cosmx/.config.vsh.yaml
+++ b/target/nextflow/filter/subset_cosmx/.config.vsh.yaml
@@ -231,7 +231,7 @@ build_info:
  output: "target/nextflow/filter/subset_cosmx"
  executable: "target/nextflow/filter/subset_cosmx/main.nf"
  viash_version: "0.9.4"
-  git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
+  git_commit: "33c1a3afb0dfebceff25b0a0104bf16582611716"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/filter/subset_cosmx/main.nf
+++ b/target/nextflow/filter/subset_cosmx/main.nf
@@ -3339,7 +3339,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/filter/subset_cosmx",
    "viash_version" : "0.9.4",
-    "git_commit" : "226d7de695d56f116dd1ba8e08a51ebf63b153b3",
+    "git_commit" : "33c1a3afb0dfebceff25b0a0104bf16582611716",
    "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
@@ -430,7 +430,7 @@ build_info:
  output: "target/nextflow/mapping/spaceranger_count"
  executable: "target/nextflow/mapping/spaceranger_count/main.nf"
  viash_version: "0.9.4"
-  git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
+  git_commit: "33c1a3afb0dfebceff25b0a0104bf16582611716"
  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
@@ -3554,7 +3554,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/mapping/spaceranger_count",
    "viash_version" : "0.9.4",
-    "git_commit" : "226d7de695d56f116dd1ba8e08a51ebf63b153b3",
+    "git_commit" : "33c1a3afb0dfebceff25b0a0104bf16582611716",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml
+++ b/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml
@@ -648,7 +648,7 @@ 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: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
+  git_commit: "33c1a3afb0dfebceff25b0a0104bf16582611716"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
  dependencies:
  - "target/dependencies/github/openpipelines-bio/openpipeline/disable-scrublet_build/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
@@ -3819,7 +3819,7 @@ meta = [
    "engine" : "native",
    "output" : "/workdir/root/repo/target/nextflow/workflows/multiomics/spatial_process_samples",
    "viash_version" : "0.9.4",
-    "git_commit" : "226d7de695d56f116dd1ba8e08a51ebf63b153b3",
+    "git_commit" : "33c1a3afb0dfebceff25b0a0104bf16582611716",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml
+++ b/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml
@@ -391,7 +391,7 @@ build_info:
  output: "target/nextflow/workflows/qc/spatial_qc"
  executable: "target/nextflow/workflows/qc/spatial_qc/main.nf"
  viash_version: "0.9.4"
-  git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
+  git_commit: "33c1a3afb0dfebceff25b0a0104bf16582611716"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
  dependencies:
  - "target/dependencies/github/openpipelines-bio/openpipeline/2.1.2/nextflow/workflows/qc/qc"
--- a/target/nextflow/workflows/qc/spatial_qc/main.nf
+++ b/target/nextflow/workflows/qc/spatial_qc/main.nf
@@ -3511,7 +3511,7 @@ meta = [
    "engine" : "native",
    "output" : "/workdir/root/repo/target/nextflow/workflows/qc/spatial_qc",
    "viash_version" : "0.9.4",
-    "git_commit" : "226d7de695d56f116dd1ba8e08a51ebf63b153b3",
+    "git_commit" : "33c1a3afb0dfebceff25b0a0104bf16582611716",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {