Build branch openpipeline_spatial/v0.1 with version v0.1.1 to openpipeline_spatial on branch v0.1 (2baba3f)

Build pipeline: openpipelines-bio.openpipeline-spatial.0.1.1-5jtw5

Source commit: 2baba3fff0

Source message: merge main

.gitignore

@@ -56,3 +56,8 @@ trace*.txt
 # vscode
 .vscode/launch.json
 .vscode/settings.json
+
+# linting
+renv.lock
+.Rprofile
+renv/

CHANGELOG.md

@@ -1,3 +1,13 @@
+# openpipeline_spatial 0.1.1
+
+## MINOR CHANGES
+
+* Add a README (PR #21).
+
+## NEW FUNCTIONALITY
+
+* `convert`: Updated multiple components to accept spatial output bundles in .zip format (for CosMx, Xenium and Aviti) as input (PR #19).
+
 # openpipeline_spatial 0.1.0
 
 ## NEW FUNCTIONALITY

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 openpipelines-bio
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -0,0 +1,55 @@
+# OpenPipeline Spatial
+
+Extensible spatial single cell analysis pipelines for reproducible and large-scale spatial single cell processing using Viash and Nextflow.
+
+OpenPipeline Spatial extends the [OpenPipeline](https://github.com/openpipelines-bio/openpipeline/) ecosystem with specialized workflows and components for spatial transcriptomics analysis. It provides standardized, reproducible pipelines that are technology-agnostic and can be used for processing spatial omics data from various technologies and platforms.
+
+[![ViashHub](https://img.shields.io/badge/ViashHub-openpipeline_spatial-7a4baa.svg)](https://www.viash-hub.com/packages/openpipeline_spatial)
+[![GitHub](https://img.shields.io/badge/GitHub-viash--hub%2Fopenpipeline_spatial-blue.svg)](https://github.com/openpipelines-bio/openpipeline_spatial)
+[![GitHub
+License](https://img.shields.io/github/license/openpipelines-bio/openpipeline_spatial.svg)](https://github.com/openpipelines-bio/openpipeline_spatial/blob/main/LICENSE)
+[![GitHub
+Issues](https://img.shields.io/github/issues/openpipelines-bio/openpipeline_spatial.svg)](https://github.com/openpipelines-bio/openpipeline_spatial/issues)
+[![Viash
+version](https://img.shields.io/badge/Viash-v0.9.3-blue.svg)](https://viash.io)
+
+## Functionality
+
+OpenPipeline Spatial executes a list of predefined tasks specifically designed for spatial omics data. These discrete steps are also provided as standalone components that can be executed individually with a standardized interface.
+
+The following spatial-specific workflows are provided:
+
+- [Ingestion](https://www.viash-hub.com/packages/openpipeline_spatial/latest/components?search=mapping): Whereas many technologies generate count matrices on-instrument, functionality is provided for the mapping & quantification of 10X Visum data.
+- [Interoperability](https://www.viash-hub.com/packages/openpipeline_spatial/latest/components?search=convert): To make sure all spatial workflows are technology-agnostic, functionality is provided to convert count matrices from different technologies (e.g. Xenium, CosMx, AtoMx, Aviti) into a common format (H5MU). In addition, functionality is provided to convert between various Spatial data formats (e.g. Seurat, SpatialExperiment, MuData, SpatialData).
+- [QC](https://www.viash-hub.com/packages/openpipeline_spatial/latest/components?search=spatial_qc): Calculation of comprehensive quality control metrics.
+- [Sample Processing](https://www.viash-hub.com/packages/openpipeline_spatial/latest/components?search=spatial_process_samples): Batch processing of multiple spatial samples, including count-based filtering, normalisation and dimensionality reduction.
+
+## Extended functionality
+
+Whereas this package only provides spatial-specific functionality, it is designed to work seamlessly with the core [OpenPipeline package](https://github.com/openpipelines-bio/openpipeline/). This means that all core OpenPipeline workflows and components can be used in conjunction with the spatial-specific ones. For example, the [**integration**](https://www.viash-hub.com/packages/openpipeline/latest/components?search=workflows%2Fintegration) and [**cell type annotation**](https://www.viash-hub.com/packages/openpipeline/latest/components?search=workflows%2Fannotation) workflows can be applied to spatial data after it has been processed using the spatial-specific workflows.
+
+``` mermaid lang="mermaid"
+flowchart LR
+  demultiplexing["Step 1: Ingestion"]
+  ingestion["Step 2: QC"]
+  process_samples["Step 3: Process Samples"]
+  integration["Step 4: Integration"]
+  downstream["Step 5: Downstream Analysis"]
+  demultiplexing-->ingestion-->process_samples-->integration-->downstream
+```
+
+## Execution via CLI or Seqera Cloud
+
+The openpipeline_spatial package is available via [Viash
+Hub](https://www.viash-hub.com/packages/openpipeline_spatial/latest/), where
+you can receive instructions on how to run the end-to-end workflow as
+well as individual subworkflows or components.
+
+It’s possible to run the workflow directly from Seqera Cloud. The necessary Nextflow schema files have been [built and provided with the workflows](https://packages.viash-hub.com/vsh/openpipeline_spatial/-/tree/build/main/target/nextflow?ref_type=heads) in order to use the form-based input. However, Seqera Cloud can not deal with multiple-value parameters for batch processing of multiple samples. Therefore, it’s better to use Viash Hub also here for launching the workflow on Seqera Cloud.
+
+* Navigate to the [Viash Hub package page](https://www.viash-hub.com/packages/openpipeline_spatial/latest/), select the workflow you want to launch and click the `launch` button.
+* Select the execution environment of choice (e.g. `Seqera Cloud`, `CLI` or `Executable`)
+* Fill in the form with the required parameters and launch the workflow.
+
+## Support
+For issues specific to spatial analysis, please use the [GitHub issues tracker](https://github.com/openpipelines-bio/openpipeline_spatial/issues). For general OpenPipeline questions, refer to the main [OpenPipeline documentation](https://openpipelines.bio/).

_viash.yaml

@@ -1,28 +1,22 @@
 viash_version: 0.9.4
-version: v0.1.0
-
+version: v0.1.1
 source: src
 target: target
-
 name: openpipeline_spatial
-organization: openpipelines-bio
-
+organization: vsh
 links:
   repository: https://github.com/openpipelines-bio/openpipeline_spatial
   docker_registry: ghcr.io
-
 repositories:
   - name: openpipeline
     repo: openpipeline
     type: vsh
     tag: v3.0.0
-
 info:
   test_resources:
     - type: s3
       path: s3://openpipelines-bio/openpipeline_spatial/resources_test
       dest: resources_test
-
-config_mods: |
+config_mods: |-
   .resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}
   .runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'

src/convert/from_cells2stats_to_h5mu/config.vsh.yaml

@@ -100,6 +100,7 @@ resources:
   - type: python_script
     path: script.py
   - path: /src/utils/setup_logger.py
+  - path: /src/utils/unzip_archived_folder.py
 
 test_resources:
   - type: python_script
@@ -118,6 +119,9 @@ engines:
         packages:
           - pyarrow
     test_setup:
+      - type: apt
+        packages:
+          - zip
       - type: python
         __merge__: [ /src/base/requirements/viashpy.yaml, .]
 

src/convert/from_cells2stats_to_h5mu/script.py

@@ -6,6 +6,8 @@ import mudata as mu
 import anndata as ad
 import re
 import json
+import zipfile
+import os
 
 ## VIASH START
 par = {
@@ -25,6 +27,8 @@ meta = {"resources_dir": "src/utils"}
 
 sys.path.append(meta["resources_dir"])
 from setup_logger import setup_logger
+from unzip_archived_folder import extract_selected_files_from_zip
+
 
 logger = setup_logger()
 
@@ -162,27 +166,43 @@ def categorize_columns(column_list, target_panel):
     )
 
 
-def main():
-    # Read data from Aviti Teton output bundle
+def retrieve_input_data(cells2stats_output_bundle):
     # Expected folder structure (showing only relevant files):
     # ├── Cytoprofiling/
     # │   └── Instrument/
     # │       └── RawCellStats.parquet
     # └── Panel.json
 
-    logger.info("Reading input data...")
-    input_dir = Path(par["input"])
-    input_data = {
-        "count_matrix": input_dir
-        / "Cytoprofiling"
-        / "Instrument"
-        / "RawCellStats.parquet",
-        "target_panel": input_dir / "Panel.json",
+    required_file_patterns = {
+        "target_panel": "**/Panel.json",
+        "count_matrix": "**/Cytoprofiling/Instrument/RawCellStats.parquet",
     }
 
-    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()}."
+    if zipfile.is_zipfile(cells2stats_output_bundle):
+        cells2stats_output_bundle = extract_selected_files_from_zip(
+            cells2stats_output_bundle, members=required_file_patterns.values()
         )
+    else:
+        cells2stats_output_bundle = Path(cells2stats_output_bundle)
+
+    assert os.path.isdir(cells2stats_output_bundle), (
+        "Input is expected to be a (compressed) directory."
+    )
+
+    input_data = {}
+    for key, pattern in required_file_patterns.items():
+        file = list(cells2stats_output_bundle.glob(pattern))
+        assert len(file) == 1, (
+            f"Expected exactly one file matching pattern {pattern}, found {len(file)}."
+        )
+        input_data[key] = file[0]
+
+    return input_data
+
+
+def main():
+    logger.info("Reading input data...")
+    input_data = retrieve_input_data(par["input"])
     with open(input_data["target_panel"], "r") as f:
         target_panel = json.load(f)
     df = pd.read_parquet(input_data["count_matrix"], engine="pyarrow")

src/convert/from_cells2stats_to_h5mu/test.py

@@ -1,6 +1,7 @@
 import pytest
 import sys
 import mudata as mu
+import subprocess
 
 ## VIASH START
 meta = {
@@ -51,6 +52,57 @@ def test_simple_execution(run_component, tmp_path):
     assert all(adata.obsm[obsm].dtype.kind == "f" for obsm in expected_obsm_keys)
 
 
+def test_compressed_input(run_component, tmp_path):
+    output = tmp_path / "aviti.h5mu"
+    zipped_input = tmp_path / "aviti.zip"
+
+    subprocess.run(
+        ["zip", "-r", str(zipped_input), "aviti"], cwd=meta["resources_dir"], check=True
+    )
+
+    # run component
+    run_component(
+        [
+            "--input",
+            zipped_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 adata.X.dtype.kind == "f"
+    expected_obs_keys = [
+        "AreaUm",
+        "Area",
+        "Tile",
+        "WellLabel",
+        "Well",
+        "Cell",
+        "NuclearAreaUm",
+        "NuclearArea",
+    ]
+    assert all([obs in expected_obs_keys for obs in adata.obs.columns])
+    obs_counts = ["Area", "Cell", "NuclearArea"]
+    assert all([adata.obs[obs].dtype.kind == "u" for obs in obs_counts])
+    obs_areas = ["AreaUm", "NuclearAreaUm"]
+    assert all([adata.obs[obs].dtype.kind == "f" for obs in obs_areas])
+    obs_categories = ["Tile", "WellLabel", "Well"]
+    assert all([adata.obs[obs].dtype.kind == "O" for obs in obs_categories])
+
+    expected_obsm_keys = ["spatial", "spatial_um"]
+    assert list(adata.obsm.keys()) == expected_obsm_keys
+    assert list(adata.uns.keys()) == expected_obsm_keys
+    assert all(adata.obsm[obsm].dtype.kind == "f" for obsm in expected_obsm_keys)
+
+
 def test_extended_parameters(run_component, tmp_path):
     output = tmp_path / "aviti_ext.h5mu"
 

src/convert/from_cosmx_to_h5mu/config.vsh.yaml

@@ -40,6 +40,8 @@ resources:
   - type: python_script
     path: script.py
   - path: /src/utils/setup_logger.py
+  - path: /src/utils/unzip_archived_folder.py
+
 test_resources:
   - type: python_script
     path: test.py
@@ -53,6 +55,10 @@ engines:
           - procps
       - type: python
         __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/squidpy.yaml]
+    test_setup:
+      - type: apt
+        packages:
+          - zip
     __merge__: [ /src/base/requirements/python_test_setup.yaml, . ]
 runners:
   - type: executable

src/convert/from_cosmx_to_h5mu/script.py

@@ -2,11 +2,12 @@ import sys
 import os
 import squidpy as sq
 import mudata as mu
-import glob
+import zipfile
+from pathlib import Path
 
 ## VIASH START
 par = {
-    "input": "./resources_test/cosmx/Lung5_Rep2_tiny",
+    "input": "./resources_test/cosmx/Lung5_Rep2_tiny.zip",
     "output": "./resources_test/cosmx/Lung5_Rep2_tiny.h5mu",
     "modality": "rna",
     "output_compression": None,
@@ -16,28 +17,57 @@ meta = {"resources_dir": "src/utils"}
 
 sys.path.append(meta["resources_dir"])
 from setup_logger import setup_logger
+from unzip_archived_folder import extract_selected_files_from_zip
 
 logger = setup_logger()
 
 
-def find_matrix_file(suffix):
-    pattern = os.path.join(par["input"], f"*{suffix}")
-    files = glob.glob(pattern)
-    assert len(files) == 1, (
-        f"Only one file matching pattern {pattern} should be present"
+def retrieve_input_data(cosmx_output_bundle):
+    # Expected folder structure (showing only relevant files):
+    # ├── *_exprMat_file.csv
+    # ├── *_fov_positions_file.csv
+    # └── *_metadata_file.csv
+
+    required_file_patterns = {
+        "counts_file": "**/*exprMat_file.csv",
+        "fov_file": "**/*fov_positions_file.csv",
+        "meta_file": "**/*metadata_file.csv",
+    }
+    if zipfile.is_zipfile(cosmx_output_bundle):
+        cosmx_output_bundle = extract_selected_files_from_zip(
+            cosmx_output_bundle, members=required_file_patterns.values()
         )
-    return files[0]
+    else:
+        cosmx_output_bundle = Path(cosmx_output_bundle)
+
+    assert os.path.isdir(cosmx_output_bundle), (
+        "Input is expected to be a (compressed) directory."
+    )
+
+    input_data = {}
+    for key, pattern in required_file_patterns.items():
+        file = list(cosmx_output_bundle.glob(pattern))
+        assert len(file) == 1, f"Expected one file for {key}, found {len(file)}."
+        input_data[key] = file[0]
+
+    return input_data
 
 
-counts_file = find_matrix_file("exprMat_file.csv")
-fov_file = find_matrix_file("fov_positions_file.csv")
-meta_file = find_matrix_file("metadata_file.csv")
-
+def main():
     logger.info("Reading in CosMx data...")
+    input_data = retrieve_input_data(par["input"])
+
     adata = sq.read.nanostring(
-    path=par["input"], counts_file=counts_file, meta_file=meta_file, fov_file=fov_file
+        path=par["input"],
+        counts_file=input_data["counts_file"],
+        meta_file=input_data["meta_file"],
+        fov_file=input_data["fov_file"],
     )
 
     logger.info("Writing output MuData object...")
     mdata = mu.MuData({par["modality"]: adata})
     mdata.write_h5mu(par["output"], compression=par["output_compression"])
+
+
+if __name__ == "__main__":
+    main()

src/convert/from_cosmx_to_h5mu/test.py

@@ -1,6 +1,7 @@
 import pytest
 import sys
 import mudata as mu
+import subprocess
 
 
 def test_simple_execution(run_component, tmp_path):
@@ -53,5 +54,62 @@ def test_simple_execution(run_component, tmp_path):
     assert adata.obsm["spatial_fov"].dtype == "float"
 
 
+def test_compressed_input(run_component, tmp_path):
+    output = tmp_path / "cosmx_tiny.h5mu"
+    zipped_input = tmp_path / "Lung5_Rep2_tiny.zip"
+
+    subprocess.run(
+        ["zip", "-r", str(zipped_input), "Lung5_Rep2_tiny"],
+        cwd=meta["resources_dir"],
+        check=True,
+    )
+
+    run_component(
+        [
+            "--input",
+            zipped_input,
+            "--dataset_id",
+            "Lung5_Rep2",
+            "--num_fovs",
+            "2",
+            "--output",
+            output,
+        ]
+    )
+    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()) == [
+        "fov",
+        "Area",
+        "AspectRatio",
+        "CenterX_global_px",
+        "CenterY_global_px",
+        "Width",
+        "Height",
+        "Mean.MembraneStain",
+        "Max.MembraneStain",
+        "Mean.PanCK",
+        "Max.PanCK",
+        "Mean.CD45",
+        "Max.CD45",
+        "Mean.CD3",
+        "Max.CD3",
+        "Mean.DAPI",
+        "Max.DAPI",
+        "cell_ID",
+    ]
+
+    assert list(adata.uns.keys()) == ["spatial"]
+    assert list(adata.obsm.keys()) == ["spatial", "spatial_fov"]
+
+    assert adata.obsm["spatial"].dtype == "int"
+    assert adata.obsm["spatial_fov"].dtype == "float"
+
+
 if __name__ == "__main__":
     sys.exit(pytest.main([__file__]))

src/convert/from_cosmx_to_spatialexperiment/config.vsh.yaml

@@ -58,6 +58,7 @@ arguments:
 resources:
   - type: r_script
     path: script.R
+  - path: /src/utils/unzip_archived_folder.R
 test_resources:
   - type: r_script
     path: test.R

src/convert/from_cosmx_to_spatialexperiment/script.R

@@ -2,7 +2,7 @@ library(SpatialExperimentIO)
 
 ### VIASH START
 par <- list(
-  input = "resources_test/cosmx/Lung5_Rep2_tiny",
+  input = "resources_test/cosmx/test2.zip",
   add_tx_path = TRUE,
   add_polygon_path = FALSE,
   add_fov_positions = TRUE,
@@ -11,16 +11,41 @@ par <- list(
   ),
   output = "spe_cosmx_test.rds"
 )
+meta <- list(
+  resources_dir = "src/utils/"
+)
 ### VIASH END
 
+source(paste0(meta$resources_dir, "/unzip_archived_folder.R"))
+
+cat("Reading input data...")
+if (tools::file_ext(par$input) == "zip") {
+  expected_file_patterns <- c(
+    "*.csv",
+    "*.parquet"
+  )
+  tmp_dir <- extract_selected_files(
+    par$input,
+    members = expected_file_patterns
+  )
+  cosmx_output_bundle <- file.path(
+    tmp_dir,
+    tools::file_path_sans_ext(basename(par$input))
+  )
+} else {
+  cosmx_output_bundle <- par$input
+}
+
+cat("Setting parameters...")
 if (par$add_polygon_path == FALSE && par$add_tx_path == FALSE) {
   add_parquet_paths <- FALSE
 } else {
   add_parquet_paths <- TRUE
 }
 
+cat("Converting to SpatialExperiment...")
 spe <- readCosmxSXE(
-  dirName = par$input,
+  dirName = cosmx_output_bundle,
   returnType = "SPE",
   countMatPattern = "exprMat_file.csv",
   metaDataPattern = "metadata_file.csv",
@@ -33,4 +58,5 @@ spe <- readCosmxSXE(
   altExps = par$alternative_experiment_features
 )
 
+cat("Saving output...")
 saveRDS(spe, file = par$output)

src/convert/from_cosmx_to_spatialexperiment/test.R

@@ -69,6 +69,74 @@ dim_input <- dim(input)
 expect_equal(dim_rds, dim_input)
 
 
+cat("> Checking execution with compressed input\n")
+
+spe <- paste0(meta[["resources_dir"]], "/Lung5_Rep2_tiny")
+out_rds <- "output.rds"
+
+create_folder_archive <- function(
+    folder_path,
+    archive = "Lung5_Rep2_tiny.zip") {
+  old_wd <- getwd()
+  on.exit(setwd(old_wd))
+  setwd(meta$resources_dir)
+  system2("zip", c("-r", archive, "Lung5_Rep2_tiny"))
+  paste0(meta$resources_dir, "/", archive)
+}
+
+zipped_spe <- create_folder_archive(spe)
+
+cat("> Running ", meta[["name"]], "\n", sep = "")
+out <- processx::run(
+  meta[["executable"]],
+  c(
+    "--input", zipped_spe,
+    "--add_tx_path", TRUE,
+    "--add_polygon_path", FALSE,
+    "--output", out_rds
+  )
+)
+
+cat("> Checking whether output file exists\n")
+expect_equal(out$status, 0)
+expect_true(file.exists(out_rds))
+
+cat("> Reading output file\n")
+obj <- readRDS(file = out_rds)
+
+cat("> Checking whether Seurat object is in the right format\n")
+# Object type
+expect_is(obj, "SpatialExperiment")
+# Assay structure
+expect_equal(names(slot(obj, "assays")), "counts")
+# Spatial coordinates
+expect_equal(
+  spatialCoordsNames(obj),
+  c("CenterX_global_px", "CenterY_global_px")
+)
+# Alternative experiments
+expect_equal(altExpNames(obj), c("NegPrb"))
+# Metadata components
+expect_named(
+  metadata(obj),
+  c("fov_positions", "transcripts"),
+  ignore.order = TRUE
+)
+# Parquet paths
+expect_true(grepl("\\.parquet$", metadata(obj)[["transcripts"]]))
+# Dimensions
+input <- readCosmxSXE(
+  dirName = spe,
+  addParquetPaths = FALSE,
+  returnType = "SPE"
+)
+
+dim_rds <- dim(obj)
+dim_input <- dim(input)
+
+expect_equal(dim_rds, dim_input)
+
+
 cat("> Checking parameter functionality\n")
 
 out_rds_ext <- "output_ext.rds"

src/convert/from_xenium_to_h5mu/config.vsh.yaml

@@ -44,6 +44,7 @@ resources:
   - type: python_script
     path: script.py
   - path: /src/utils/setup_logger.py
+  - path: /src/utils/unzip_archived_folder.py
 test_resources:
   - type: python_script
     path: test.py
@@ -60,6 +61,9 @@ engines:
         packages:
           - pyarrow
     test_setup:
+      - type: apt
+        packages:
+          - zip
       - type: python
         __merge__: [ /src/base/requirements/viashpy.yaml, .]
 runners:

src/convert/from_xenium_to_h5mu/script.py

@@ -3,11 +3,13 @@ from pathlib import Path
 import scanpy as sc
 import pandas as pd
 import mudata as mu
+import zipfile
 import json
+import os
 
 ## VIASH START
 par = {
-    "input": "./resources_test/xenium/xenium_tiny",
+    "input": "test/xenium_tiny.zip",
     "output": "xenium_tiny_test.h5mu",
     "output_compression": "gzip",
     "obsm_coordinates": "spatial",
@@ -19,22 +21,47 @@ meta = {"resources_dir": "src/utils"}
 
 sys.path.append(meta["resources_dir"])
 from setup_logger import setup_logger
+from unzip_archived_folder import extract_selected_files_from_zip
 
 logger = setup_logger()
 
+
+def _retrieve_input_data(xenium_output_bundle):
     # 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",
+
+    required_file_patterns = {
+        "count_matrix": "**/cell_feature_matrix.h5",
+        "cells_metadata": "**/cells.parquet",
+        "experiment": "**/experiment.xenium",
+        "metrics_summary": "**/metrics_summary.csv",
     }
 
+    if zipfile.is_zipfile(xenium_output_bundle):
+        xenium_output_bundle = extract_selected_files_from_zip(
+            xenium_output_bundle,
+            members=[pattern for pattern in required_file_patterns.values()],
+        )
+    else:
+        xenium_output_bundle = Path(xenium_output_bundle)
+
+    assert os.path.isdir(xenium_output_bundle), (
+        "Input is expected to be a (compressed) directory."
+    )
+
+    input_data = {}
+    for key, pattern in required_file_patterns.items():
+        file = list(xenium_output_bundle.glob(pattern))
+        assert len(file) == 1, (
+            f"Expected exactly one file matching pattern {pattern}, found {len(file)}."
+        )
+        input_data[key] = file[0]
+
+    return input_data
+
 
 def _format_cell_id_column(cell_id_column: pd.Series) -> pd.Series:
     """Convert cell IDs to string format, decoding bytes if necessary."""
@@ -46,9 +73,7 @@ def _format_cell_id_column(cell_id_column: pd.Series) -> pd.Series:
 # 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()}."
-)
+input_data = _retrieve_input_data(par["input"])
 
 adata = sc.read_10x_h5(input_data["count_matrix"])
 metadata = pd.read_parquet(input_data["cells_metadata"], engine="pyarrow")

src/convert/from_xenium_to_h5mu/test.py

@@ -1,12 +1,13 @@
 import pytest
 import sys
+import subprocess
 import mudata as mu
 
 ## VIASH START
 meta = {
-    "executable": "./target/executable/convert/from_cellranger_multi_to_h5mu/from_cellranger_multi_to_h5mu",
+    "executable": "./target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu",
     "resources_dir": "resources_test/",
-    "config": "src/convert/from_cellranger_multi_to_h5mu/config.vsh.yaml",
+    "config": "src/convert/from_xenium_to_h5mu/config.vsh.yaml",
 }
 ## VIASH END
 
@@ -62,6 +63,69 @@ def test_simple_execution(run_component, tmp_path):
     assert all([adata.obs[obs].dtype == "float" for obs in obs_areas])
 
 
+def test_compressed_input(run_component, tmp_path):
+    output = tmp_path / "xenium.h5mu"
+    zipped_input = tmp_path / "xenium_tiny.zip"
+
+    subprocess.run(
+        ["zip", "-r", str(zipped_input), "xenium_tiny"],
+        cwd=meta["resources_dir"],
+        check=True,
+    )
+
+    # run component
+    run_component(
+        [
+            "--input",
+            zipped_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"
 

src/convert/from_xenium_to_spatialdata/config.vsh.yaml

@@ -78,6 +78,7 @@ resources:
   - type: python_script
     path: script.py
   - path: /src/utils/setup_logger.py
+  - path: /src/utils/unzip_archived_folder.py
 test_resources:
   - type: python_script
     path: test.py
@@ -91,6 +92,10 @@ engines:
           - procps
       - type: python
         __merge__: [ /src/base/requirements/spatialdata-io.yaml ]
+    test_setup:
+      - type: apt
+        packages:
+          - zip
     __merge__: [ /src/base/requirements/python_test_setup.yaml, .]
 runners:
   - type: executable

src/convert/from_xenium_to_spatialdata/script.py

@@ -1,9 +1,11 @@
 import sys
 from spatialdata_io import xenium
+import zipfile
+from pathlib import Path
 
 ## VIASH START
 par = {
-    "input": "./resources_test/xenium_tiny",
+    "input": "xenium_tiny.zip",
     "output": "./test/xenium_tiny.zarr",
     "cells_boundaries": True,
     "nucleus_boundaries": True,
@@ -22,12 +24,29 @@ meta = {"resources_dir": "src/utils"}
 
 sys.path.append(meta["resources_dir"])
 from setup_logger import setup_logger
+from unzip_archived_folder import unzip_archived_folder
 
 logger = setup_logger()
 
 logger.info("Reading in Xenium data...")
+
+if zipfile.is_zipfile(par["input"]):
+    required_file_patterns = [
+        "**/experiment.xenium",
+        "**/nucleus_boundaries.parquet",
+        "**/cell_boundaries.parquet",
+        "**/transcripts.parquet",
+        "**/cell_feature_matrix.h5",
+        "**/cells.parquet",
+        "**/morphology_mip.ome.tif",
+        "**/morphology_focus.ome.tif",
+    ]
+    xenium_output_bundle = unzip_archived_folder(par["input"])
+else:
+    xenium_output_bundle = Path(par["input"])
+
 sdata = xenium(
-    par["input"],
+    xenium_output_bundle,
     cells_boundaries=par["cells_boundaries"],
     nucleus_boundaries=par["nucleus_boundaries"],
     cells_as_circles=par["cells_as_circles"],

src/convert/from_xenium_to_spatialdata/test.py

@@ -2,6 +2,7 @@ import pytest
 import os
 import sys
 import spatialdata as sd
+import subprocess
 
 
 def test_simple_execution(run_component, tmp_path):
@@ -31,5 +32,38 @@ def test_simple_execution(run_component, tmp_path):
     assert (output_sd_path / "zmetadata").is_file(), "zmetadata file was not created"
 
 
+def test_compressed_input(run_component, tmp_path):
+    output_sd_path = tmp_path / "sd"
+    zipped_input = tmp_path / "xenium_tiny.zip"
+
+    subprocess.run(
+        ["zip", "-r", str(zipped_input), "xenium_tiny"],
+        cwd=meta["resources_dir"],
+        check=True,
+    )
+    run_component(
+        [
+            "--input",
+            zipped_input,
+            "--output",
+            output_sd_path,
+        ]
+    )
+
+    assert os.path.exists(output_sd_path), "Output zarr folder was not created"
+
+    sdata = sd.read_zarr(output_sd_path)
+    assert isinstance(sdata, sd.SpatialData), (
+        "the generated output is not a SpatialData object"
+    )
+
+    assert os.path.exists(output_sd_path / "images"), "images folder was not created"
+    assert os.path.exists(output_sd_path / "labels"), "labels folder was not created"
+    assert os.path.exists(output_sd_path / "points"), "images folder was not created"
+    assert os.path.exists(output_sd_path / "shapes"), "shapes folder was not created"
+    assert os.path.exists(output_sd_path / "tables"), "tables folder was not created"
+    assert (output_sd_path / "zmetadata").is_file(), "zmetadata file was not created"
+
+
 if __name__ == "__main__":
     sys.exit(pytest.main([__file__]))

src/convert/from_xenium_to_spatialexperiment/config.vsh.yaml

@@ -51,6 +51,7 @@ arguments:
 resources:
   - type: r_script
     path: script.R
+  - path: /src/utils/unzip_archived_folder.R
 test_resources:
   - type: r_script
     path: test.R

src/convert/from_xenium_to_spatialexperiment/script.R

@@ -2,7 +2,7 @@ library(SpatialExperimentIO)
 
 ### VIASH START
 par <- list(
-  input = "resources_test/xenium/xenium_tiny",
+  input = "resources_test/xenium/temp_dir.zip",
   add_experiment_xenium = TRUE,
   add_parquet_paths = TRUE,
   alternative_experiment_features = c(
@@ -11,11 +11,35 @@ par <- list(
   ),
   output = "spe_test.rds"
 )
+meta <- list(
+  resources_dir = "src/utils/"
+)
 ### VIASH END
 
+source(paste0(meta$resources_dir, "/unzip_archived_folder.R"))
 
+cat("Reading input data...")
+if (tools::file_ext(par$input) == "zip") {
+  required_file_patterns <- c(
+    "**/cell_feature_matrix.h5",
+    "**/*.parquet",
+    "**/experiment.xenium"
+  )
+  tmp_dir <- extract_selected_files(
+    par$input,
+    members = required_file_patterns
+  )
+  xenium_output_bundle <- file.path(
+    tmp_dir,
+    tools::file_path_sans_ext(basename(par$input))
+  )
+} else {
+  xenium_output_bundle <- par$input
+}
+
+cat("Converting to SpatialExperiment")
 spe <- readXeniumSXE(
-  dirName = par$input,
+  dirName = xenium_output_bundle,
   returnType = "SPE",
   countMatPattern = "cell_feature_matrix.h5",
   metaDataPattern = "cells.parquet",
@@ -25,4 +49,5 @@ spe <- readXeniumSXE(
   altExps = par$alternative_experiment_features
 )
 
+cat("Saving output...")
 saveRDS(spe, file = par$output)

src/convert/from_xenium_to_spatialexperiment/test.R

@@ -71,6 +71,77 @@ dim_input <- dim(input)
 expect_equal(dim_rds, dim_input)
 
 
+cat("> Checking execution with compressed input\n")
+
+spe <- paste0(
+  meta[["resources_dir"]],
+  "/xenium_tiny"
+)
+out_rds <- "output.rds"
+
+create_folder_archive <- function(folder_path, archive = "xenium_tiny.zip") {
+  old_wd <- getwd()
+  on.exit(setwd(old_wd))
+  setwd(meta$resources_dir)
+  system2("zip", c("-r", archive, "xenium_tiny"))
+  paste0(meta$resources_dir, "/", archive)
+}
+
+zipped_spe <- create_folder_archive(spe)
+
+cat("> Running ", meta[["name"]], "\n", sep = "")
+out <- processx::run(
+  meta[["executable"]],
+  c(
+    "--input", zipped_spe,
+    "--output", out_rds
+  )
+)
+
+cat("> Checking whether output file exists\n")
+expect_equal(out$status, 0)
+expect_true(file.exists(out_rds))
+
+cat("> Reading output file\n")
+obj <- readRDS(file = out_rds)
+
+cat("> Checking whether Seurat object is in the right format\n")
+# Object type
+expect_is(obj, "SpatialExperiment")
+# Assay structure
+expect_equal(names(slot(obj, "assays")), "counts")
+# Spatial coordinates
+expect_equal(spatialCoordsNames(obj), c("x_centroid", "y_centroid"))
+# Alternative experiments
+expect_equal(
+  altExpNames(obj),
+  c("NegControlProbe", "UnassignedCodeword", "NegControlCodeword")
+)
+# Metadata components
+metadata_components <- c(
+  "experiment.xenium", "transcripts", "cell_boundaries", "nucleus_boundaries"
+)
+expect_named(
+  metadata(obj),
+  metadata_components,
+  ignore.order = TRUE
+)
+# Parquet paths
+parquet_components <- c("transcripts", "cell_boundaries", "nucleus_boundaries")
+for (component in parquet_components) {
+  expect_true(grepl("\\.parquet$", metadata(obj)[[component]]))
+}
+# Dimensions
+input <- readXeniumSXE(
+  dirName = spe,
+  returnType = "SPE"
+)
+dim_rds <- dim(obj)
+dim_input <- dim(input)
+
+expect_equal(dim_rds, dim_input)
+
+
 cat("> Checking parameter functionality\n")
 
 out_rds_ext <- "output_ext.rds"

src/utils/unzip_archived_folder.R

@@ -0,0 +1,22 @@
+extract_selected_files <- function(zip_path, members) {
+  # Create a temporary directory for extraction
+  temp_dir <- tempfile("unzip_dir_")
+  dir.create(temp_dir)
+
+  # List all files in the archive
+  all_files <- utils::unzip(zip_path, list = TRUE)$Name
+
+  # Find files matching any of the glob patterns in 'members'
+  selected <- unique(unlist(
+    lapply(members, function(pattern) {
+      regex <- glob2rx(pattern)
+      grep(regex, all_files, value = TRUE)
+    })
+  ))
+
+  # Extract only the selected files
+  utils::unzip(zip_path, files = selected, exdir = temp_dir)
+
+  # Return the path to the extracted folder
+  file.path(temp_dir)
+}

src/utils/unzip_archived_folder.py

@@ -0,0 +1,50 @@
+import fnmatch
+import zipfile
+import tempfile
+from pathlib import Path
+from typing import Union
+
+
+def unzip_archived_folder(archived_folder: Union[str, Path]) -> Union[str, Path]:
+    """
+    Extracts a ZIP archive to a temporary directory and returns the path to the extracted folder.
+
+    Args:
+        zip_path (Union[str, Path]): Path to the ZIP archive.
+
+    Returns:
+        extracted_path (Union[str, Path]): Path to the extracted folder inside the temporary directory.
+    """
+
+    temp_dir = Path(tempfile.TemporaryDirectory().name)
+    with zipfile.ZipFile(archived_folder, "r") as archive:
+        archive.extractall(temp_dir)
+
+    return temp_dir / Path(archived_folder).stem
+
+
+def extract_selected_files_from_zip(
+    zip_path: Union[str, Path], members: list[Union[str, Path]]
+) -> Union[str, Path]:
+    """
+    Extracts selected files (supports glob patterns) from a ZIP archive to a temporary directory.
+
+    Args:
+        zip_path (Union[str, Path]): Path to the ZIP archive.
+        members (list[str]): List of file paths within the archive to extract.
+
+    Returns:
+        Path: Path to the extraction directory.
+    """
+
+    temp_dir = Path(tempfile.TemporaryDirectory().name)
+
+    with zipfile.ZipFile(zip_path, "r") as archive:
+        all_files = archive.namelist()
+        selected = set()
+        for pattern in members:
+            selected.update(fnmatch.filter(all_files, str(pattern)))
+        for member in selected:
+            archive.extract(member, temp_dir)
+
+    return temp_dir

target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "from_cells2stats_to_h5mu"
 namespace: "convert"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -150,6 +150,8 @@ resources:
   is_executable: true
 - type: "file"
   path: "setup_logger.py"
+- type: "file"
+  path: "unzip_archived_folder.py"
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
@@ -256,7 +258,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -274,6 +276,10 @@ engines:
       nelse:  exit(1)\")"
     upgrade: true
   test_setup:
+  - type: "apt"
+    packages:
+    - "zip"
+    interactive: false
   - type: "python"
     user: false
     packages:
@@ -290,11 +296,11 @@ 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: "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
+  git_commit: "2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -314,7 +320,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   organization: "vsh"
   links:
     repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# from_cells2stats_to_h5mu v0.1.0
+# from_cells2stats_to_h5mu v0.1.1
 # 
 # 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
@@ -458,10 +458,10 @@ 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="2025-08-25T12:22:56Z"
+LABEL org.opencontainers.image.created="2025-10-02T08:36:59Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.revision="2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
+LABEL org.opencontainers.image.version="v0.1.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "from_cells2stats_to_h5mu v0.1.0"
+  echo "from_cells2stats_to_h5mu v0.1.1"
   echo ""
   echo "Convert spatial data resulting from Aviti Teton sequencers that have been"
   echo "processed by the Element Biosciences cells2stats workflow to H5MU format."
@@ -722,7 +722,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "from_cells2stats_to_h5mu v0.1.0"
+            echo "from_cells2stats_to_h5mu v0.1.1"
             exit
             ;;
         --input)
@@ -923,7 +923,7 @@ if [[ "$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/convert/from_cells2stats_to_h5mu:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/convert/from_cells2stats_to_h5mu:v0.1.1'
   fi
 
   # print dockerfile
@@ -1242,6 +1242,8 @@ import mudata as mu
 import anndata as ad
 import re
 import json
+import zipfile
+import os
 
 ## VIASH START
 # The following code has been auto-generated by Viash.
@@ -1285,6 +1287,8 @@ dep = {
 
 sys.path.append(meta["resources_dir"])
 from setup_logger import setup_logger
+from unzip_archived_folder import extract_selected_files_from_zip
+
 
 logger = setup_logger()
 
@@ -1422,27 +1426,43 @@ def categorize_columns(column_list, target_panel):
     )
 
 
-def main():
-    # Read data from Aviti Teton output bundle
+def retrieve_input_data(cells2stats_output_bundle):
     # Expected folder structure (showing only relevant files):
     # ├── Cytoprofiling/
     # │   └── Instrument/
     # │       └── RawCellStats.parquet
     # └── Panel.json
 
-    logger.info("Reading input data...")
-    input_dir = Path(par["input"])
-    input_data = {
-        "count_matrix": input_dir
-        / "Cytoprofiling"
-        / "Instrument"
-        / "RawCellStats.parquet",
-        "target_panel": input_dir / "Panel.json",
+    required_file_patterns = {
+        "target_panel": "**/Panel.json",
+        "count_matrix": "**/Cytoprofiling/Instrument/RawCellStats.parquet",
     }
 
-    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()}."
+    if zipfile.is_zipfile(cells2stats_output_bundle):
+        cells2stats_output_bundle = extract_selected_files_from_zip(
+            cells2stats_output_bundle, members=required_file_patterns.values()
         )
+    else:
+        cells2stats_output_bundle = Path(cells2stats_output_bundle)
+
+    assert os.path.isdir(cells2stats_output_bundle), (
+        "Input is expected to be a (compressed) directory."
+    )
+
+    input_data = {}
+    for key, pattern in required_file_patterns.items():
+        file = list(cells2stats_output_bundle.glob(pattern))
+        assert len(file) == 1, (
+            f"Expected exactly one file matching pattern {pattern}, found {len(file)}."
+        )
+        input_data[key] = file[0]
+
+    return input_data
+
+
+def main():
+    logger.info("Reading input data...")
+    input_data = retrieve_input_data(par["input"])
     with open(input_data["target_panel"], "r") as f:
         target_panel = json.load(f)
     df = pd.read_parquet(input_data["count_matrix"], engine="pyarrow")

target/executable/convert/from_cells2stats_to_h5mu/unzip_archived_folder.py

@@ -0,0 +1,50 @@
+import fnmatch
+import zipfile
+import tempfile
+from pathlib import Path
+from typing import Union
+
+
+def unzip_archived_folder(archived_folder: Union[str, Path]) -> Union[str, Path]:
+    """
+    Extracts a ZIP archive to a temporary directory and returns the path to the extracted folder.
+
+    Args:
+        zip_path (Union[str, Path]): Path to the ZIP archive.
+
+    Returns:
+        extracted_path (Union[str, Path]): Path to the extracted folder inside the temporary directory.
+    """
+
+    temp_dir = Path(tempfile.TemporaryDirectory().name)
+    with zipfile.ZipFile(archived_folder, "r") as archive:
+        archive.extractall(temp_dir)
+
+    return temp_dir / Path(archived_folder).stem
+
+
+def extract_selected_files_from_zip(
+    zip_path: Union[str, Path], members: list[Union[str, Path]]
+) -> Union[str, Path]:
+    """
+    Extracts selected files (supports glob patterns) from a ZIP archive to a temporary directory.
+
+    Args:
+        zip_path (Union[str, Path]): Path to the ZIP archive.
+        members (list[str]): List of file paths within the archive to extract.
+
+    Returns:
+        Path: Path to the extraction directory.
+    """
+
+    temp_dir = Path(tempfile.TemporaryDirectory().name)
+
+    with zipfile.ZipFile(zip_path, "r") as archive:
+        all_files = archive.namelist()
+        selected = set()
+        for pattern in members:
+            selected.update(fnmatch.filter(all_files, str(pattern)))
+        for member in selected:
+            archive.extract(member, temp_dir)
+
+    return temp_dir

target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "from_cosmx_to_h5mu"
 namespace: "convert"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -81,6 +81,8 @@ resources:
   is_executable: true
 - type: "file"
   path: "setup_logger.py"
+- type: "file"
+  path: "unzip_archived_folder.py"
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
@@ -184,7 +186,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -214,6 +216,10 @@ engines:
     github:
     - "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
     upgrade: true
+  - type: "apt"
+    packages:
+    - "zip"
+    interactive: false
   entrypoint: []
   cmd: null
 - type: "native"
@@ -225,11 +231,11 @@ 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: "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
+  git_commit: "2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -249,7 +255,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   organization: "vsh"
   links:
     repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# from_cosmx_to_h5mu v0.1.0
+# from_cosmx_to_h5mu v0.1.1
 # 
 # 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
@@ -459,10 +459,10 @@ 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="2025-08-25T12:22:57Z"
+LABEL org.opencontainers.image.created="2025-10-02T08:37:01Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.revision="2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
+LABEL org.opencontainers.image.version="v0.1.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "from_cosmx_to_h5mu v0.1.0"
+  echo "from_cosmx_to_h5mu v0.1.1"
   echo ""
   echo "Converts the output from NanoString experiment into a MuData objcet."
   echo "  - \`<dataset_id>_exprMat_file.csv\`: File containing the counts."
@@ -658,7 +658,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "from_cosmx_to_h5mu v0.1.0"
+            echo "from_cosmx_to_h5mu v0.1.1"
             exit
             ;;
         --input)
@@ -805,7 +805,7 @@ if [[ "$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/convert/from_cosmx_to_h5mu:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/convert/from_cosmx_to_h5mu:v0.1.1'
   fi
 
   # print dockerfile
@@ -1113,7 +1113,8 @@ import sys
 import os
 import squidpy as sq
 import mudata as mu
-import glob
+import zipfile
+from pathlib import Path
 
 ## VIASH START
 # The following code has been auto-generated by Viash.
@@ -1151,31 +1152,60 @@ dep = {
 
 sys.path.append(meta["resources_dir"])
 from setup_logger import setup_logger
+from unzip_archived_folder import extract_selected_files_from_zip
 
 logger = setup_logger()
 
 
-def find_matrix_file(suffix):
-    pattern = os.path.join(par["input"], f"*{suffix}")
-    files = glob.glob(pattern)
-    assert len(files) == 1, (
-        f"Only one file matching pattern {pattern} should be present"
+def retrieve_input_data(cosmx_output_bundle):
+    # Expected folder structure (showing only relevant files):
+    # ├── *_exprMat_file.csv
+    # ├── *_fov_positions_file.csv
+    # └── *_metadata_file.csv
+
+    required_file_patterns = {
+        "counts_file": "**/*exprMat_file.csv",
+        "fov_file": "**/*fov_positions_file.csv",
+        "meta_file": "**/*metadata_file.csv",
+    }
+    if zipfile.is_zipfile(cosmx_output_bundle):
+        cosmx_output_bundle = extract_selected_files_from_zip(
+            cosmx_output_bundle, members=required_file_patterns.values()
         )
-    return files[0]
+    else:
+        cosmx_output_bundle = Path(cosmx_output_bundle)
+
+    assert os.path.isdir(cosmx_output_bundle), (
+        "Input is expected to be a (compressed) directory."
+    )
+
+    input_data = {}
+    for key, pattern in required_file_patterns.items():
+        file = list(cosmx_output_bundle.glob(pattern))
+        assert len(file) == 1, f"Expected one file for {key}, found {len(file)}."
+        input_data[key] = file[0]
+
+    return input_data
 
 
-counts_file = find_matrix_file("exprMat_file.csv")
-fov_file = find_matrix_file("fov_positions_file.csv")
-meta_file = find_matrix_file("metadata_file.csv")
-
+def main():
     logger.info("Reading in CosMx data...")
+    input_data = retrieve_input_data(par["input"])
+
     adata = sq.read.nanostring(
-    path=par["input"], counts_file=counts_file, meta_file=meta_file, fov_file=fov_file
+        path=par["input"],
+        counts_file=input_data["counts_file"],
+        meta_file=input_data["meta_file"],
+        fov_file=input_data["fov_file"],
     )
 
     logger.info("Writing output MuData object...")
     mdata = mu.MuData({par["modality"]: adata})
     mdata.write_h5mu(par["output"], compression=par["output_compression"])
+
+
+if __name__ == "__main__":
+    main()
 VIASHMAIN
 python -B "\$tempscript" &
 wait "\$!"

target/executable/convert/from_cosmx_to_h5mu/unzip_archived_folder.py

@@ -0,0 +1,50 @@
+import fnmatch
+import zipfile
+import tempfile
+from pathlib import Path
+from typing import Union
+
+
+def unzip_archived_folder(archived_folder: Union[str, Path]) -> Union[str, Path]:
+    """
+    Extracts a ZIP archive to a temporary directory and returns the path to the extracted folder.
+
+    Args:
+        zip_path (Union[str, Path]): Path to the ZIP archive.
+
+    Returns:
+        extracted_path (Union[str, Path]): Path to the extracted folder inside the temporary directory.
+    """
+
+    temp_dir = Path(tempfile.TemporaryDirectory().name)
+    with zipfile.ZipFile(archived_folder, "r") as archive:
+        archive.extractall(temp_dir)
+
+    return temp_dir / Path(archived_folder).stem
+
+
+def extract_selected_files_from_zip(
+    zip_path: Union[str, Path], members: list[Union[str, Path]]
+) -> Union[str, Path]:
+    """
+    Extracts selected files (supports glob patterns) from a ZIP archive to a temporary directory.
+
+    Args:
+        zip_path (Union[str, Path]): Path to the ZIP archive.
+        members (list[str]): List of file paths within the archive to extract.
+
+    Returns:
+        Path: Path to the extraction directory.
+    """
+
+    temp_dir = Path(tempfile.TemporaryDirectory().name)
+
+    with zipfile.ZipFile(zip_path, "r") as archive:
+        all_files = archive.namelist()
+        selected = set()
+        for pattern in members:
+            selected.update(fnmatch.filter(all_files, str(pattern)))
+        for member in selected:
+            archive.extract(member, temp_dir)
+
+    return temp_dir

target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "from_cosmx_to_spatialexperiment"
 namespace: "convert"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -98,6 +98,8 @@ resources:
 - type: "r_script"
   path: "script.R"
   is_executable: true
+- type: "file"
+  path: "unzip_archived_folder.R"
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
@@ -202,7 +204,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -232,11 +234,11 @@ 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: "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
+  git_commit: "2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -256,7 +258,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   organization: "vsh"
   links:
     repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# from_cosmx_to_spatialexperiment v0.1.0
+# from_cosmx_to_spatialexperiment v0.1.1
 # 
 # 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
@@ -457,10 +457,10 @@ 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="2025-08-25T12:22:56Z"
+LABEL org.opencontainers.image.created="2025-10-02T08:37:00Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.revision="2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
+LABEL org.opencontainers.image.version="v0.1.1"
 
 VIASHDOCKER
   fi
@@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "from_cosmx_to_spatialexperiment v0.1.0"
+  echo "from_cosmx_to_spatialexperiment v0.1.1"
   echo ""
   echo "Creates a SpatialExperiment object from the downloaded unzipped CosMx directory"
   echo "for Nanostring"
@@ -678,7 +678,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "from_cosmx_to_spatialexperiment v0.1.0"
+            echo "from_cosmx_to_spatialexperiment v0.1.1"
             exit
             ;;
         --input)
@@ -853,7 +853,7 @@ if [[ "$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/convert/from_cosmx_to_spatialexperiment:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/convert/from_cosmx_to_spatialexperiment:v0.1.1'
   fi
 
   # print dockerfile
@@ -1221,14 +1221,36 @@ rm(.viash_orig_warn)
 
 ### VIASH END
 
+source(paste0(meta\$resources_dir, "/unzip_archived_folder.R"))
+
+cat("Reading input data...")
+if (tools::file_ext(par\$input) == "zip") {
+  expected_file_patterns <- c(
+    "*.csv",
+    "*.parquet"
+  )
+  tmp_dir <- extract_selected_files(
+    par\$input,
+    members = expected_file_patterns
+  )
+  cosmx_output_bundle <- file.path(
+    tmp_dir,
+    tools::file_path_sans_ext(basename(par\$input))
+  )
+} else {
+  cosmx_output_bundle <- par\$input
+}
+
+cat("Setting parameters...")
 if (par\$add_polygon_path == FALSE && par\$add_tx_path == FALSE) {
   add_parquet_paths <- FALSE
 } else {
   add_parquet_paths <- TRUE
 }
 
+cat("Converting to SpatialExperiment...")
 spe <- readCosmxSXE(
-  dirName = par\$input,
+  dirName = cosmx_output_bundle,
   returnType = "SPE",
   countMatPattern = "exprMat_file.csv",
   metaDataPattern = "metadata_file.csv",
@@ -1241,6 +1263,7 @@ spe <- readCosmxSXE(
   altExps = par\$alternative_experiment_features
 )
 
+cat("Saving output...")
 saveRDS(spe, file = par\$output)
 VIASHMAIN
 Rscript "\$tempscript" &

target/executable/convert/from_cosmx_to_spatialexperiment/unzip_archived_folder.R

@@ -0,0 +1,22 @@
+extract_selected_files <- function(zip_path, members) {
+  # Create a temporary directory for extraction
+  temp_dir <- tempfile("unzip_dir_")
+  dir.create(temp_dir)
+
+  # List all files in the archive
+  all_files <- utils::unzip(zip_path, list = TRUE)$Name
+
+  # Find files matching any of the glob patterns in 'members'
+  selected <- unique(unlist(
+    lapply(members, function(pattern) {
+      regex <- glob2rx(pattern)
+      grep(regex, all_files, value = TRUE)
+    })
+  ))
+
+  # Extract only the selected files
+  utils::unzip(zip_path, files = selected, exdir = temp_dir)
+
+  # Return the path to the extracted folder
+  file.path(temp_dir)
+}

target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "from_h5mu_to_spatialexperiment"
 namespace: "convert"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -171,7 +171,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:22.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -224,11 +224,11 @@ 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: "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
+  git_commit: "2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -248,7 +248,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   organization: "vsh"
   links:
     repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# from_h5mu_to_spatialexperiment v0.1.0
+# from_h5mu_to_spatialexperiment v0.1.1
 # 
 # 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
@@ -458,10 +458,10 @@ 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="2025-08-25T12:22:57Z"
+LABEL org.opencontainers.image.created="2025-10-02T08:37:00Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.revision="2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
+LABEL org.opencontainers.image.version="v0.1.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "from_h5mu_to_spatialexperiment v0.1.0"
+  echo "from_h5mu_to_spatialexperiment v0.1.1"
   echo ""
   echo "Converts an h5mu file into a SpatialExperiment object."
   echo ""
@@ -650,7 +650,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "from_h5mu_to_spatialexperiment v0.1.0"
+            echo "from_h5mu_to_spatialexperiment v0.1.1"
             exit
             ;;
         --input)
@@ -797,7 +797,7 @@ if [[ "$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/convert/from_h5mu_to_spatialexperiment:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/convert/from_h5mu_to_spatialexperiment:v0.1.1'
   fi
 
   # print dockerfile

target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "from_spatialdata_to_h5mu"
 namespace: "convert"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -180,7 +180,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -220,11 +220,11 @@ 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: "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
+  git_commit: "2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -244,7 +244,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   organization: "vsh"
   links:
     repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# from_spatialdata_to_h5mu v0.1.0
+# from_spatialdata_to_h5mu v0.1.1
 # 
 # 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
@@ -459,10 +459,10 @@ 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="2025-08-25T12:22:56Z"
+LABEL org.opencontainers.image.created="2025-10-02T08:37:00Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.revision="2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
+LABEL org.opencontainers.image.version="v0.1.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "from_spatialdata_to_h5mu v0.1.0"
+  echo "from_spatialdata_to_h5mu v0.1.1"
   echo ""
   echo "Reads in the Tables field stored in a SpatialData object and converts it to an"
   echo "h5mu file."
@@ -651,7 +651,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "from_spatialdata_to_h5mu v0.1.0"
+            echo "from_spatialdata_to_h5mu v0.1.1"
             exit
             ;;
         --input)
@@ -798,7 +798,7 @@ if [[ "$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/convert/from_spatialdata_to_h5mu:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/convert/from_spatialdata_to_h5mu:v0.1.1'
   fi
 
   # print dockerfile

target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "from_xenium_to_h5mu"
 namespace: "convert"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -97,6 +97,8 @@ resources:
   is_executable: true
 - type: "file"
   path: "setup_logger.py"
+- type: "file"
+  path: "unzip_archived_folder.py"
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
@@ -198,7 +200,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -217,6 +219,10 @@ engines:
       nelse:  exit(1)\")"
     upgrade: true
   test_setup:
+  - type: "apt"
+    packages:
+    - "zip"
+    interactive: false
   - type: "python"
     user: false
     packages:
@@ -233,11 +239,11 @@ 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: "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
+  git_commit: "2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -257,7 +263,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   organization: "vsh"
   links:
     repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# from_xenium_to_h5mu v0.1.0
+# from_xenium_to_h5mu v0.1.1
 # 
 # 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
@@ -458,10 +458,10 @@ 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="2025-08-25T12:22:56Z"
+LABEL org.opencontainers.image.created="2025-10-02T08:37:00Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.revision="2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
+LABEL org.opencontainers.image.version="v0.1.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "from_xenium_to_h5mu v0.1.0"
+  echo "from_xenium_to_h5mu v0.1.1"
   echo ""
   echo "Converts the output from Xenium to a single .h5mu file, where the count matrix"
   echo "is written to the \`rna\` modality."
@@ -670,7 +670,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "from_xenium_to_h5mu v0.1.0"
+            echo "from_xenium_to_h5mu v0.1.1"
             exit
             ;;
         --input)
@@ -839,7 +839,7 @@ if [[ "$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/convert/from_xenium_to_h5mu:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/convert/from_xenium_to_h5mu:v0.1.1'
   fi
 
   # print dockerfile
@@ -1154,7 +1154,9 @@ from pathlib import Path
 import scanpy as sc
 import pandas as pd
 import mudata as mu
+import zipfile
 import json
+import os
 
 ## VIASH START
 # The following code has been auto-generated by Viash.
@@ -1194,22 +1196,47 @@ dep = {
 
 sys.path.append(meta["resources_dir"])
 from setup_logger import setup_logger
+from unzip_archived_folder import extract_selected_files_from_zip
 
 logger = setup_logger()
 
+
+def _retrieve_input_data(xenium_output_bundle):
     # 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",
+
+    required_file_patterns = {
+        "count_matrix": "**/cell_feature_matrix.h5",
+        "cells_metadata": "**/cells.parquet",
+        "experiment": "**/experiment.xenium",
+        "metrics_summary": "**/metrics_summary.csv",
     }
 
+    if zipfile.is_zipfile(xenium_output_bundle):
+        xenium_output_bundle = extract_selected_files_from_zip(
+            xenium_output_bundle,
+            members=[pattern for pattern in required_file_patterns.values()],
+        )
+    else:
+        xenium_output_bundle = Path(xenium_output_bundle)
+
+    assert os.path.isdir(xenium_output_bundle), (
+        "Input is expected to be a (compressed) directory."
+    )
+
+    input_data = {}
+    for key, pattern in required_file_patterns.items():
+        file = list(xenium_output_bundle.glob(pattern))
+        assert len(file) == 1, (
+            f"Expected exactly one file matching pattern {pattern}, found {len(file)}."
+        )
+        input_data[key] = file[0]
+
+    return input_data
+
 
 def _format_cell_id_column(cell_id_column: pd.Series) -> pd.Series:
     """Convert cell IDs to string format, decoding bytes if necessary."""
@@ -1221,9 +1248,7 @@ def _format_cell_id_column(cell_id_column: pd.Series) -> pd.Series:
 # 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()}."
-)
+input_data = _retrieve_input_data(par["input"])
 
 adata = sc.read_10x_h5(input_data["count_matrix"])
 metadata = pd.read_parquet(input_data["cells_metadata"], engine="pyarrow")

target/executable/convert/from_xenium_to_h5mu/unzip_archived_folder.py

@@ -0,0 +1,50 @@
+import fnmatch
+import zipfile
+import tempfile
+from pathlib import Path
+from typing import Union
+
+
+def unzip_archived_folder(archived_folder: Union[str, Path]) -> Union[str, Path]:
+    """
+    Extracts a ZIP archive to a temporary directory and returns the path to the extracted folder.
+
+    Args:
+        zip_path (Union[str, Path]): Path to the ZIP archive.
+
+    Returns:
+        extracted_path (Union[str, Path]): Path to the extracted folder inside the temporary directory.
+    """
+
+    temp_dir = Path(tempfile.TemporaryDirectory().name)
+    with zipfile.ZipFile(archived_folder, "r") as archive:
+        archive.extractall(temp_dir)
+
+    return temp_dir / Path(archived_folder).stem
+
+
+def extract_selected_files_from_zip(
+    zip_path: Union[str, Path], members: list[Union[str, Path]]
+) -> Union[str, Path]:
+    """
+    Extracts selected files (supports glob patterns) from a ZIP archive to a temporary directory.
+
+    Args:
+        zip_path (Union[str, Path]): Path to the ZIP archive.
+        members (list[str]): List of file paths within the archive to extract.
+
+    Returns:
+        Path: Path to the extraction directory.
+    """
+
+    temp_dir = Path(tempfile.TemporaryDirectory().name)
+
+    with zipfile.ZipFile(zip_path, "r") as archive:
+        all_files = archive.namelist()
+        selected = set()
+        for pattern in members:
+            selected.update(fnmatch.filter(all_files, str(pattern)))
+        for member in selected:
+            archive.extract(member, temp_dir)
+
+    return temp_dir

target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "from_xenium_to_spatialdata"
 namespace: "convert"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -173,6 +173,8 @@ resources:
   is_executable: true
 - type: "file"
   path: "setup_logger.py"
+- type: "file"
+  path: "unzip_archived_folder.py"
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
@@ -278,7 +280,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -303,6 +305,10 @@ engines:
     github:
     - "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
     upgrade: true
+  - type: "apt"
+    packages:
+    - "zip"
+    interactive: false
   entrypoint: []
   cmd: null
 - type: "native"
@@ -314,11 +320,11 @@ 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: "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
+  git_commit: "2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -338,7 +344,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   organization: "vsh"
   links:
     repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# from_xenium_to_spatialdata v0.1.0
+# from_xenium_to_spatialdata v0.1.1
 # 
 # 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
@@ -458,10 +458,10 @@ 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="2025-08-25T12:22:57Z"
+LABEL org.opencontainers.image.created="2025-10-02T08:36:59Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.revision="2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
+LABEL org.opencontainers.image.version="v0.1.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "from_xenium_to_spatialdata v0.1.0"
+  echo "from_xenium_to_spatialdata v0.1.1"
   echo ""
   echo "Converts the output from 10X Genomics Xenium dataset into a SpatialData objcet."
   echo "By default, the following files will be converted:"
@@ -711,7 +711,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "from_xenium_to_spatialdata v0.1.0"
+            echo "from_xenium_to_spatialdata v0.1.1"
             exit
             ;;
         --input)
@@ -951,7 +951,7 @@ if [[ "$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/convert/from_xenium_to_spatialdata:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/convert/from_xenium_to_spatialdata:v0.1.1'
   fi
 
   # print dockerfile
@@ -1340,6 +1340,8 @@ trap interrupt INT SIGINT
 cat > "\$tempscript" << 'VIASHMAIN'
 import sys
 from spatialdata_io import xenium
+import zipfile
+from pathlib import Path
 
 ## VIASH START
 # The following code has been auto-generated by Viash.
@@ -1386,12 +1388,29 @@ dep = {
 
 sys.path.append(meta["resources_dir"])
 from setup_logger import setup_logger
+from unzip_archived_folder import unzip_archived_folder
 
 logger = setup_logger()
 
 logger.info("Reading in Xenium data...")
+
+if zipfile.is_zipfile(par["input"]):
+    required_file_patterns = [
+        "**/experiment.xenium",
+        "**/nucleus_boundaries.parquet",
+        "**/cell_boundaries.parquet",
+        "**/transcripts.parquet",
+        "**/cell_feature_matrix.h5",
+        "**/cells.parquet",
+        "**/morphology_mip.ome.tif",
+        "**/morphology_focus.ome.tif",
+    ]
+    xenium_output_bundle = unzip_archived_folder(par["input"])
+else:
+    xenium_output_bundle = Path(par["input"])
+
 sdata = xenium(
-    par["input"],
+    xenium_output_bundle,
     cells_boundaries=par["cells_boundaries"],
     nucleus_boundaries=par["nucleus_boundaries"],
     cells_as_circles=par["cells_as_circles"],

target/executable/convert/from_xenium_to_spatialdata/unzip_archived_folder.py

@@ -0,0 +1,50 @@
+import fnmatch
+import zipfile
+import tempfile
+from pathlib import Path
+from typing import Union
+
+
+def unzip_archived_folder(archived_folder: Union[str, Path]) -> Union[str, Path]:
+    """
+    Extracts a ZIP archive to a temporary directory and returns the path to the extracted folder.
+
+    Args:
+        zip_path (Union[str, Path]): Path to the ZIP archive.
+
+    Returns:
+        extracted_path (Union[str, Path]): Path to the extracted folder inside the temporary directory.
+    """
+
+    temp_dir = Path(tempfile.TemporaryDirectory().name)
+    with zipfile.ZipFile(archived_folder, "r") as archive:
+        archive.extractall(temp_dir)
+
+    return temp_dir / Path(archived_folder).stem
+
+
+def extract_selected_files_from_zip(
+    zip_path: Union[str, Path], members: list[Union[str, Path]]
+) -> Union[str, Path]:
+    """
+    Extracts selected files (supports glob patterns) from a ZIP archive to a temporary directory.
+
+    Args:
+        zip_path (Union[str, Path]): Path to the ZIP archive.
+        members (list[str]): List of file paths within the archive to extract.
+
+    Returns:
+        Path: Path to the extraction directory.
+    """
+
+    temp_dir = Path(tempfile.TemporaryDirectory().name)
+
+    with zipfile.ZipFile(zip_path, "r") as archive:
+        all_files = archive.namelist()
+        selected = set()
+        for pattern in members:
+            selected.update(fnmatch.filter(all_files, str(pattern)))
+        for member in selected:
+            archive.extract(member, temp_dir)
+
+    return temp_dir

target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "from_xenium_to_spatialexperiment"
 namespace: "convert"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -88,6 +88,8 @@ resources:
 - type: "r_script"
   path: "script.R"
   is_executable: true
+- type: "file"
+  path: "unzip_archived_folder.R"
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
@@ -192,7 +194,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -222,11 +224,11 @@ 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: "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
+  git_commit: "2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -246,7 +248,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   organization: "vsh"
   links:
     repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# from_xenium_to_spatialexperiment v0.1.0
+# from_xenium_to_spatialexperiment v0.1.1
 # 
 # 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
@@ -457,10 +457,10 @@ 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="2025-08-25T12:22:56Z"
+LABEL org.opencontainers.image.created="2025-10-02T08:37:00Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.revision="2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
+LABEL org.opencontainers.image.version="v0.1.1"
 
 VIASHDOCKER
   fi
@@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "from_xenium_to_spatialexperiment v0.1.0"
+  echo "from_xenium_to_spatialexperiment v0.1.1"
   echo ""
   echo "Creates a SpatialExperiment object from the downloaded unzipped Xenium Output"
   echo "Bundle directory"
@@ -673,7 +673,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "from_xenium_to_spatialexperiment v0.1.0"
+            echo "from_xenium_to_spatialexperiment v0.1.1"
             exit
             ;;
         --input)
@@ -837,7 +837,7 @@ if [[ "$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/convert/from_xenium_to_spatialexperiment:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/convert/from_xenium_to_spatialexperiment:v0.1.1'
   fi
 
   # print dockerfile
@@ -1195,9 +1195,30 @@ rm(.viash_orig_warn)
 
 ### VIASH END
 
+source(paste0(meta\$resources_dir, "/unzip_archived_folder.R"))
 
+cat("Reading input data...")
+if (tools::file_ext(par\$input) == "zip") {
+  required_file_patterns <- c(
+    "**/cell_feature_matrix.h5",
+    "**/*.parquet",
+    "**/experiment.xenium"
+  )
+  tmp_dir <- extract_selected_files(
+    par\$input,
+    members = required_file_patterns
+  )
+  xenium_output_bundle <- file.path(
+    tmp_dir,
+    tools::file_path_sans_ext(basename(par\$input))
+  )
+} else {
+  xenium_output_bundle <- par\$input
+}
+
+cat("Converting to SpatialExperiment")
 spe <- readXeniumSXE(
-  dirName = par\$input,
+  dirName = xenium_output_bundle,
   returnType = "SPE",
   countMatPattern = "cell_feature_matrix.h5",
   metaDataPattern = "cells.parquet",
@@ -1207,6 +1228,7 @@ spe <- readXeniumSXE(
   altExps = par\$alternative_experiment_features
 )
 
+cat("Saving output...")
 saveRDS(spe, file = par\$output)
 VIASHMAIN
 Rscript "\$tempscript" &

target/executable/convert/from_xenium_to_spatialexperiment/unzip_archived_folder.R

@@ -0,0 +1,22 @@
+extract_selected_files <- function(zip_path, members) {
+  # Create a temporary directory for extraction
+  temp_dir <- tempfile("unzip_dir_")
+  dir.create(temp_dir)
+
+  # List all files in the archive
+  all_files <- utils::unzip(zip_path, list = TRUE)$Name
+
+  # Find files matching any of the glob patterns in 'members'
+  selected <- unique(unlist(
+    lapply(members, function(pattern) {
+      regex <- glob2rx(pattern)
+      grep(regex, all_files, value = TRUE)
+    })
+  ))
+
+  # Extract only the selected files
+  utils::unzip(zip_path, files = selected, exdir = temp_dir)
+
+  # Return the path to the extracted folder
+  file.path(temp_dir)
+}

target/executable/filter/subset_cosmx/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "subset_cosmx"
 namespace: "filter"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -191,7 +191,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -227,11 +227,11 @@ build_info:
   output: "target/executable/filter/subset_cosmx"
   executable: "target/executable/filter/subset_cosmx/subset_cosmx"
   viash_version: "0.9.4"
-  git_commit: "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
+  git_commit: "2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -251,7 +251,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   organization: "vsh"
   links:
     repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

target/executable/filter/subset_cosmx/subset_cosmx

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# subset_cosmx v0.1.0
+# subset_cosmx v0.1.1
 # 
 # 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
@@ -458,10 +458,10 @@ 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="2025-08-25T12:22:56Z"
+LABEL org.opencontainers.image.created="2025-10-02T08:36:59Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.revision="2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
+LABEL org.opencontainers.image.version="v0.1.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "subset_cosmx v0.1.0"
+  echo "subset_cosmx v0.1.1"
   echo ""
   echo "Filters the output from NanoString experiment to keep only a subset of the"
   echo "fields of view."
@@ -666,7 +666,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "subset_cosmx v0.1.0"
+            echo "subset_cosmx v0.1.1"
             exit
             ;;
         --input)
@@ -824,7 +824,7 @@ if [[ "$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/filter/subset_cosmx:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/filter/subset_cosmx:v0.1.1'
   fi
 
   # print dockerfile

target/executable/mapping/spaceranger_count/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "spaceranger_count"
 namespace: "mapping"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Jakub Majercik"
   roles:
@@ -408,7 +408,7 @@ engines:
   id: "docker"
   image: "ghcr.io/data-intuitive/spaceranger:3.1"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -426,11 +426,11 @@ build_info:
   output: "target/executable/mapping/spaceranger_count"
   executable: "target/executable/mapping/spaceranger_count/spaceranger_count"
   viash_version: "0.9.4"
-  git_commit: "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
+  git_commit: "2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -450,7 +450,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   organization: "vsh"
   links:
     repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

target/executable/mapping/spaceranger_count/spaceranger_count

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# spaceranger_count v0.1.0
+# spaceranger_count v0.1.1
 # 
 # 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
@@ -453,10 +453,10 @@ 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="2025-08-25T12:22:57Z"
+LABEL org.opencontainers.image.created="2025-10-02T08:36:59Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.revision="2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
+LABEL org.opencontainers.image.version="v0.1.1"
 
 VIASHDOCKER
   fi
@@ -573,7 +573,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "spaceranger_count v0.1.0"
+  echo "spaceranger_count v0.1.1"
   echo ""
   echo "Count gene expression and protein expression reads from a single capture area."
   echo ""
@@ -775,7 +775,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "spaceranger_count v0.1.0"
+            echo "spaceranger_count v0.1.1"
             exit
             ;;
         --gex_reference)
@@ -1135,7 +1135,7 @@ if [[ "$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/mapping/spaceranger_count:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/mapping/spaceranger_count:v0.1.1'
   fi
 
   # print dockerfile

target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "from_cells2stats_to_h5mu"
 namespace: "convert"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -150,6 +150,8 @@ resources:
   is_executable: true
 - type: "file"
   path: "setup_logger.py"
+- type: "file"
+  path: "unzip_archived_folder.py"
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
@@ -256,7 +258,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -274,6 +276,10 @@ engines:
       nelse:  exit(1)\")"
     upgrade: true
   test_setup:
+  - type: "apt"
+    packages:
+    - "zip"
+    interactive: false
   - type: "python"
     user: false
     packages:
@@ -290,11 +296,11 @@ 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: "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
+  git_commit: "2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -314,7 +320,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   organization: "vsh"
   links:
     repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

target/nextflow/convert/from_cells2stats_to_h5mu/main.nf

@@ -1,4 +1,4 @@
-// from_cells2stats_to_h5mu v0.1.0
+// from_cells2stats_to_h5mu v0.1.1
 // 
 // 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
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "from_cells2stats_to_h5mu",
   "namespace" : "convert",
-  "version" : "v0.1.0",
+  "version" : "v0.1.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3214,6 +3214,10 @@ meta = [
       "type" : "file",
       "path" : "/src/utils/setup_logger.py"
     },
+    {
+      "type" : "file",
+      "path" : "/src/utils/unzip_archived_folder.py"
+    },
     {
       "type" : "file",
       "path" : "/src/workflows/utils/labels.config",
@@ -3336,7 +3340,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.13-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.1.0",
+      "target_tag" : "v0.1.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3361,6 +3365,13 @@ meta = [
         }
       ],
       "test_setup" : [
+        {
+          "type" : "apt",
+          "packages" : [
+            "zip"
+          ],
+          "interactive" : false
+        },
         {
           "type" : "python",
           "user" : false,
@@ -3382,12 +3393,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_cells2stats_to_h5mu",
     "viash_version" : "0.9.4",
-    "git_commit" : "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36",
+    "git_commit" : "2baba3fff0930478c26da7e1bd99b29ee5dd83b3",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
     "name" : "openpipeline_spatial",
-    "version" : "v0.1.0",
+    "version" : "v0.1.1",
     "info" : {
       "test_resources" : [
         {
@@ -3412,7 +3423,7 @@ meta = [
       ".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 := 'v0.1.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
     ],
     "organization" : "vsh",
     "links" : {
@@ -3440,6 +3451,8 @@ import mudata as mu
 import anndata as ad
 import re
 import json
+import zipfile
+import os
 
 ## VIASH START
 # The following code has been auto-generated by Viash.
@@ -3483,6 +3496,8 @@ dep = {
 
 sys.path.append(meta["resources_dir"])
 from setup_logger import setup_logger
+from unzip_archived_folder import extract_selected_files_from_zip
+
 
 logger = setup_logger()
 
@@ -3620,27 +3635,43 @@ def categorize_columns(column_list, target_panel):
     )
 
 
-def main():
-    # Read data from Aviti Teton output bundle
+def retrieve_input_data(cells2stats_output_bundle):
     # Expected folder structure (showing only relevant files):
     # ├── Cytoprofiling/
     # │   └── Instrument/
     # │       └── RawCellStats.parquet
     # └── Panel.json
 
-    logger.info("Reading input data...")
-    input_dir = Path(par["input"])
-    input_data = {
-        "count_matrix": input_dir
-        / "Cytoprofiling"
-        / "Instrument"
-        / "RawCellStats.parquet",
-        "target_panel": input_dir / "Panel.json",
+    required_file_patterns = {
+        "target_panel": "**/Panel.json",
+        "count_matrix": "**/Cytoprofiling/Instrument/RawCellStats.parquet",
     }
 
-    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()}."
+    if zipfile.is_zipfile(cells2stats_output_bundle):
+        cells2stats_output_bundle = extract_selected_files_from_zip(
+            cells2stats_output_bundle, members=required_file_patterns.values()
         )
+    else:
+        cells2stats_output_bundle = Path(cells2stats_output_bundle)
+
+    assert os.path.isdir(cells2stats_output_bundle), (
+        "Input is expected to be a (compressed) directory."
+    )
+
+    input_data = {}
+    for key, pattern in required_file_patterns.items():
+        file = list(cells2stats_output_bundle.glob(pattern))
+        assert len(file) == 1, (
+            f"Expected exactly one file matching pattern {pattern}, found {len(file)}."
+        )
+        input_data[key] = file[0]
+
+    return input_data
+
+
+def main():
+    logger.info("Reading input data...")
+    input_data = retrieve_input_data(par["input"])
     with open(input_data["target_panel"], "r") as f:
         target_panel = json.load(f)
     df = pd.read_parquet(input_data["count_matrix"], engine="pyarrow")
@@ -4123,7 +4154,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline_spatial/convert/from_cells2stats_to_h5mu",
-    "tag" : "v0.1.0"
+    "tag" : "v0.1.1"
   },
   "label" : [
     "lowmem",

target/nextflow/convert/from_cells2stats_to_h5mu/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'convert/from_cells2stats_to_h5mu'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = 'v0.1.1'
   description = 'Convert spatial data resulting from Aviti Teton sequencers that have been processed by the Element Biosciences cells2stats workflow to H5MU format.\n\nThis component processes cells2stats count matrices to create a standardized H5MU file for downstream analysis.\n\nThe component reads:\n- Parquet file containing the count matrix and metadata\n- Panel.json with target and batch information\n\nAnd outputs an H5MU file with:\n- Count data as the main .X matrix\n- Spatial coordinates in obsm\n- Cell Paint intensities in obsm (optional)\n- Nuclear count data as a layer (optional)\n- CellProfiler morphology metrics in obsm (optional)\n- Unassigned targets in obsm (optional)\n'
   author = 'Dorien Roosen'
 }

target/nextflow/convert/from_cells2stats_to_h5mu/unzip_archived_folder.py

@@ -0,0 +1,50 @@
+import fnmatch
+import zipfile
+import tempfile
+from pathlib import Path
+from typing import Union
+
+
+def unzip_archived_folder(archived_folder: Union[str, Path]) -> Union[str, Path]:
+    """
+    Extracts a ZIP archive to a temporary directory and returns the path to the extracted folder.
+
+    Args:
+        zip_path (Union[str, Path]): Path to the ZIP archive.
+
+    Returns:
+        extracted_path (Union[str, Path]): Path to the extracted folder inside the temporary directory.
+    """
+
+    temp_dir = Path(tempfile.TemporaryDirectory().name)
+    with zipfile.ZipFile(archived_folder, "r") as archive:
+        archive.extractall(temp_dir)
+
+    return temp_dir / Path(archived_folder).stem
+
+
+def extract_selected_files_from_zip(
+    zip_path: Union[str, Path], members: list[Union[str, Path]]
+) -> Union[str, Path]:
+    """
+    Extracts selected files (supports glob patterns) from a ZIP archive to a temporary directory.
+
+    Args:
+        zip_path (Union[str, Path]): Path to the ZIP archive.
+        members (list[str]): List of file paths within the archive to extract.
+
+    Returns:
+        Path: Path to the extraction directory.
+    """
+
+    temp_dir = Path(tempfile.TemporaryDirectory().name)
+
+    with zipfile.ZipFile(zip_path, "r") as archive:
+        all_files = archive.namelist()
+        selected = set()
+        for pattern in members:
+            selected.update(fnmatch.filter(all_files, str(pattern)))
+        for member in selected:
+            archive.extract(member, temp_dir)
+
+    return temp_dir

target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "from_cosmx_to_h5mu"
 namespace: "convert"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -81,6 +81,8 @@ resources:
   is_executable: true
 - type: "file"
   path: "setup_logger.py"
+- type: "file"
+  path: "unzip_archived_folder.py"
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
@@ -184,7 +186,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -214,6 +216,10 @@ engines:
     github:
     - "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
     upgrade: true
+  - type: "apt"
+    packages:
+    - "zip"
+    interactive: false
   entrypoint: []
   cmd: null
 - type: "native"
@@ -225,11 +231,11 @@ 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: "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
+  git_commit: "2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -249,7 +255,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   organization: "vsh"
   links:
     repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

target/nextflow/convert/from_cosmx_to_h5mu/main.nf

@@ -1,4 +1,4 @@
-// from_cosmx_to_h5mu v0.1.0
+// from_cosmx_to_h5mu v0.1.1
 // 
 // 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
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "from_cosmx_to_h5mu",
   "namespace" : "convert",
-  "version" : "v0.1.0",
+  "version" : "v0.1.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3152,6 +3152,10 @@ meta = [
       "type" : "file",
       "path" : "/src/utils/setup_logger.py"
     },
+    {
+      "type" : "file",
+      "path" : "/src/utils/unzip_archived_folder.py"
+    },
     {
       "type" : "file",
       "path" : "/src/workflows/utils/labels.config",
@@ -3274,7 +3278,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.1.0",
+      "target_tag" : "v0.1.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3317,6 +3321,13 @@ meta = [
             "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
           ],
           "upgrade" : true
+        },
+        {
+          "type" : "apt",
+          "packages" : [
+            "zip"
+          ],
+          "interactive" : false
         }
       ]
     },
@@ -3331,12 +3342,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_h5mu",
     "viash_version" : "0.9.4",
-    "git_commit" : "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36",
+    "git_commit" : "2baba3fff0930478c26da7e1bd99b29ee5dd83b3",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
     "name" : "openpipeline_spatial",
-    "version" : "v0.1.0",
+    "version" : "v0.1.1",
     "info" : {
       "test_resources" : [
         {
@@ -3361,7 +3372,7 @@ meta = [
       ".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 := 'v0.1.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
     ],
     "organization" : "vsh",
     "links" : {
@@ -3385,7 +3396,8 @@ import sys
 import os
 import squidpy as sq
 import mudata as mu
-import glob
+import zipfile
+from pathlib import Path
 
 ## VIASH START
 # The following code has been auto-generated by Viash.
@@ -3423,31 +3435,60 @@ dep = {
 
 sys.path.append(meta["resources_dir"])
 from setup_logger import setup_logger
+from unzip_archived_folder import extract_selected_files_from_zip
 
 logger = setup_logger()
 
 
-def find_matrix_file(suffix):
-    pattern = os.path.join(par["input"], f"*{suffix}")
-    files = glob.glob(pattern)
-    assert len(files) == 1, (
-        f"Only one file matching pattern {pattern} should be present"
+def retrieve_input_data(cosmx_output_bundle):
+    # Expected folder structure (showing only relevant files):
+    # ├── *_exprMat_file.csv
+    # ├── *_fov_positions_file.csv
+    # └── *_metadata_file.csv
+
+    required_file_patterns = {
+        "counts_file": "**/*exprMat_file.csv",
+        "fov_file": "**/*fov_positions_file.csv",
+        "meta_file": "**/*metadata_file.csv",
+    }
+    if zipfile.is_zipfile(cosmx_output_bundle):
+        cosmx_output_bundle = extract_selected_files_from_zip(
+            cosmx_output_bundle, members=required_file_patterns.values()
         )
-    return files[0]
+    else:
+        cosmx_output_bundle = Path(cosmx_output_bundle)
+
+    assert os.path.isdir(cosmx_output_bundle), (
+        "Input is expected to be a (compressed) directory."
+    )
+
+    input_data = {}
+    for key, pattern in required_file_patterns.items():
+        file = list(cosmx_output_bundle.glob(pattern))
+        assert len(file) == 1, f"Expected one file for {key}, found {len(file)}."
+        input_data[key] = file[0]
+
+    return input_data
 
 
-counts_file = find_matrix_file("exprMat_file.csv")
-fov_file = find_matrix_file("fov_positions_file.csv")
-meta_file = find_matrix_file("metadata_file.csv")
-
+def main():
     logger.info("Reading in CosMx data...")
+    input_data = retrieve_input_data(par["input"])
+
     adata = sq.read.nanostring(
-    path=par["input"], counts_file=counts_file, meta_file=meta_file, fov_file=fov_file
+        path=par["input"],
+        counts_file=input_data["counts_file"],
+        meta_file=input_data["meta_file"],
+        fov_file=input_data["fov_file"],
     )
 
     logger.info("Writing output MuData object...")
     mdata = mu.MuData({par["modality"]: adata})
     mdata.write_h5mu(par["output"], compression=par["output_compression"])
+
+
+if __name__ == "__main__":
+    main()
 VIASHMAIN
 python -B "$tempscript"
 '''
@@ -3830,7 +3871,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline_spatial/convert/from_cosmx_to_h5mu",
-    "tag" : "v0.1.0"
+    "tag" : "v0.1.1"
   },
   "label" : [
     "lowmem",

target/nextflow/convert/from_cosmx_to_h5mu/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'convert/from_cosmx_to_h5mu'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = 'v0.1.1'
   description = 'Converts the output from NanoString experiment into a MuData objcet.\n  - `<dataset_id>_exprMat_file.csv`: File containing the counts.\n  - `<dataset_id>`_metadata_file: File containing the spatial coordinates and additional cell-level metadata.\n  - `<dataset_id>_fov_file.csv`: File containing the coordinates of all the fields of view.\nIn addition to reading the regular Nanostring output, it loads CellComposite and CellLabels directories, if present,\ncontaining the images.\n'
   author = 'Dorien Roosen, Weiwei Schultz'
 }

target/nextflow/convert/from_cosmx_to_h5mu/unzip_archived_folder.py

@@ -0,0 +1,50 @@
+import fnmatch
+import zipfile
+import tempfile
+from pathlib import Path
+from typing import Union
+
+
+def unzip_archived_folder(archived_folder: Union[str, Path]) -> Union[str, Path]:
+    """
+    Extracts a ZIP archive to a temporary directory and returns the path to the extracted folder.
+
+    Args:
+        zip_path (Union[str, Path]): Path to the ZIP archive.
+
+    Returns:
+        extracted_path (Union[str, Path]): Path to the extracted folder inside the temporary directory.
+    """
+
+    temp_dir = Path(tempfile.TemporaryDirectory().name)
+    with zipfile.ZipFile(archived_folder, "r") as archive:
+        archive.extractall(temp_dir)
+
+    return temp_dir / Path(archived_folder).stem
+
+
+def extract_selected_files_from_zip(
+    zip_path: Union[str, Path], members: list[Union[str, Path]]
+) -> Union[str, Path]:
+    """
+    Extracts selected files (supports glob patterns) from a ZIP archive to a temporary directory.
+
+    Args:
+        zip_path (Union[str, Path]): Path to the ZIP archive.
+        members (list[str]): List of file paths within the archive to extract.
+
+    Returns:
+        Path: Path to the extraction directory.
+    """
+
+    temp_dir = Path(tempfile.TemporaryDirectory().name)
+
+    with zipfile.ZipFile(zip_path, "r") as archive:
+        all_files = archive.namelist()
+        selected = set()
+        for pattern in members:
+            selected.update(fnmatch.filter(all_files, str(pattern)))
+        for member in selected:
+            archive.extract(member, temp_dir)
+
+    return temp_dir

target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "from_cosmx_to_spatialexperiment"
 namespace: "convert"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -98,6 +98,8 @@ resources:
 - type: "r_script"
   path: "script.R"
   is_executable: true
+- type: "file"
+  path: "unzip_archived_folder.R"
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
@@ -202,7 +204,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -232,11 +234,11 @@ 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: "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
+  git_commit: "2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -256,7 +258,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   organization: "vsh"
   links:
     repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf

@@ -1,4 +1,4 @@
-// from_cosmx_to_spatialexperiment v0.1.0
+// from_cosmx_to_spatialexperiment v0.1.1
 // 
 // 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
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "from_cosmx_to_spatialexperiment",
   "namespace" : "convert",
-  "version" : "v0.1.0",
+  "version" : "v0.1.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3158,6 +3158,10 @@ meta = [
       "path" : "script.R",
       "is_executable" : true
     },
+    {
+      "type" : "file",
+      "path" : "/src/utils/unzip_archived_folder.R"
+    },
     {
       "type" : "file",
       "path" : "/src/workflows/utils/labels.config",
@@ -3280,7 +3284,7 @@ meta = [
       "id" : "docker",
       "image" : "rocker/r2u:24.04",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.1.0",
+      "target_tag" : "v0.1.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3322,12 +3326,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_spatialexperiment",
     "viash_version" : "0.9.4",
-    "git_commit" : "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36",
+    "git_commit" : "2baba3fff0930478c26da7e1bd99b29ee5dd83b3",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
     "name" : "openpipeline_spatial",
-    "version" : "v0.1.0",
+    "version" : "v0.1.1",
     "info" : {
       "test_resources" : [
         {
@@ -3352,7 +3356,7 @@ meta = [
       ".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 := 'v0.1.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
     ],
     "organization" : "vsh",
     "links" : {
@@ -3418,14 +3422,36 @@ rm(.viash_orig_warn)
 
 ### VIASH END
 
+source(paste0(meta\\$resources_dir, "/unzip_archived_folder.R"))
+
+cat("Reading input data...")
+if (tools::file_ext(par\\$input) == "zip") {
+  expected_file_patterns <- c(
+    "*.csv",
+    "*.parquet"
+  )
+  tmp_dir <- extract_selected_files(
+    par\\$input,
+    members = expected_file_patterns
+  )
+  cosmx_output_bundle <- file.path(
+    tmp_dir,
+    tools::file_path_sans_ext(basename(par\\$input))
+  )
+} else {
+  cosmx_output_bundle <- par\\$input
+}
+
+cat("Setting parameters...")
 if (par\\$add_polygon_path == FALSE && par\\$add_tx_path == FALSE) {
   add_parquet_paths <- FALSE
 } else {
   add_parquet_paths <- TRUE
 }
 
+cat("Converting to SpatialExperiment...")
 spe <- readCosmxSXE(
-  dirName = par\\$input,
+  dirName = cosmx_output_bundle,
   returnType = "SPE",
   countMatPattern = "exprMat_file.csv",
   metaDataPattern = "metadata_file.csv",
@@ -3438,6 +3464,7 @@ spe <- readCosmxSXE(
   altExps = par\\$alternative_experiment_features
 )
 
+cat("Saving output...")
 saveRDS(spe, file = par\\$output)
 VIASHMAIN
 Rscript "$tempscript"
@@ -3821,7 +3848,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline_spatial/convert/from_cosmx_to_spatialexperiment",
-    "tag" : "v0.1.0"
+    "tag" : "v0.1.1"
   },
   "label" : [
     "lowmem",

target/nextflow/convert/from_cosmx_to_spatialexperiment/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'convert/from_cosmx_to_spatialexperiment'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = 'v0.1.1'
   description = 'Creates a SpatialExperiment object from the downloaded unzipped CosMx directory for Nanostring\nCosMx spatial gene expression data, and saves it as a SpatialExperiment object.\nThe constructor assumes the downloaded unzipped CosMx Folder has the following structure:\n\nMandatory files\n· | — *_exprMat_file.csv\n· | — *_metadata_file.csv\nOptional files, by default added to the metadata() as a list of paths (will be converted to parquet):\n· | —*_fov_positions_file.csv\n· | — *_tx_file.csv\n· | — *_polygons.csv\n'
   author = 'Dorien Roosen'
 }

target/nextflow/convert/from_cosmx_to_spatialexperiment/unzip_archived_folder.R

@@ -0,0 +1,22 @@
+extract_selected_files <- function(zip_path, members) {
+  # Create a temporary directory for extraction
+  temp_dir <- tempfile("unzip_dir_")
+  dir.create(temp_dir)
+
+  # List all files in the archive
+  all_files <- utils::unzip(zip_path, list = TRUE)$Name
+
+  # Find files matching any of the glob patterns in 'members'
+  selected <- unique(unlist(
+    lapply(members, function(pattern) {
+      regex <- glob2rx(pattern)
+      grep(regex, all_files, value = TRUE)
+    })
+  ))
+
+  # Extract only the selected files
+  utils::unzip(zip_path, files = selected, exdir = temp_dir)
+
+  # Return the path to the extracted folder
+  file.path(temp_dir)
+}

target/nextflow/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "from_h5mu_to_spatialexperiment"
 namespace: "convert"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -171,7 +171,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:22.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -224,11 +224,11 @@ 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: "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
+  git_commit: "2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -248,7 +248,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   organization: "vsh"
   links:
     repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf

@@ -1,4 +1,4 @@
-// from_h5mu_to_spatialexperiment v0.1.0
+// from_h5mu_to_spatialexperiment v0.1.1
 // 
 // 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
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "from_h5mu_to_spatialexperiment",
   "namespace" : "convert",
-  "version" : "v0.1.0",
+  "version" : "v0.1.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3257,7 +3257,7 @@ meta = [
       "id" : "docker",
       "image" : "rocker/r2u:22.04",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.1.0",
+      "target_tag" : "v0.1.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3332,12 +3332,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_h5mu_to_spatialexperiment",
     "viash_version" : "0.9.4",
-    "git_commit" : "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36",
+    "git_commit" : "2baba3fff0930478c26da7e1bd99b29ee5dd83b3",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
     "name" : "openpipeline_spatial",
-    "version" : "v0.1.0",
+    "version" : "v0.1.1",
     "info" : {
       "test_resources" : [
         {
@@ -3362,7 +3362,7 @@ meta = [
       ".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 := 'v0.1.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
     ],
     "organization" : "vsh",
     "links" : {
@@ -3910,7 +3910,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline_spatial/convert/from_h5mu_to_spatialexperiment",
-    "tag" : "v0.1.0"
+    "tag" : "v0.1.1"
   },
   "label" : [
     "lowmem",

target/nextflow/convert/from_h5mu_to_spatialexperiment/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'convert/from_h5mu_to_spatialexperiment'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = 'v0.1.1'
   description = 'Converts an h5mu file into a SpatialExperiment object.\n'
   author = 'Dorien Roosen'
 }

target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "from_spatialdata_to_h5mu"
 namespace: "convert"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -180,7 +180,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -220,11 +220,11 @@ 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: "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
+  git_commit: "2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -244,7 +244,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   organization: "vsh"
   links:
     repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

target/nextflow/convert/from_spatialdata_to_h5mu/main.nf

@@ -1,4 +1,4 @@
-// from_spatialdata_to_h5mu v0.1.0
+// from_spatialdata_to_h5mu v0.1.1
 // 
 // 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
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "from_spatialdata_to_h5mu",
   "namespace" : "convert",
-  "version" : "v0.1.0",
+  "version" : "v0.1.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3274,7 +3274,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.1.0",
+      "target_tag" : "v0.1.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3330,12 +3330,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_spatialdata_to_h5mu",
     "viash_version" : "0.9.4",
-    "git_commit" : "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36",
+    "git_commit" : "2baba3fff0930478c26da7e1bd99b29ee5dd83b3",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
     "name" : "openpipeline_spatial",
-    "version" : "v0.1.0",
+    "version" : "v0.1.1",
     "info" : {
       "test_resources" : [
         {
@@ -3360,7 +3360,7 @@ meta = [
       ".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 := 'v0.1.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
     ],
     "organization" : "vsh",
     "links" : {
@@ -3814,7 +3814,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline_spatial/convert/from_spatialdata_to_h5mu",
-    "tag" : "v0.1.0"
+    "tag" : "v0.1.1"
   },
   "label" : [
     "lowmem",

target/nextflow/convert/from_spatialdata_to_h5mu/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'convert/from_spatialdata_to_h5mu'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = 'v0.1.1'
   description = 'Reads in the Tables field stored in a SpatialData object and converts it to an h5mu file.\n  \n'
   author = 'Dorien Roosen, Weiwei Schultz'
 }

target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "from_xenium_to_h5mu"
 namespace: "convert"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -97,6 +97,8 @@ resources:
   is_executable: true
 - type: "file"
   path: "setup_logger.py"
+- type: "file"
+  path: "unzip_archived_folder.py"
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
@@ -198,7 +200,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -217,6 +219,10 @@ engines:
       nelse:  exit(1)\")"
     upgrade: true
   test_setup:
+  - type: "apt"
+    packages:
+    - "zip"
+    interactive: false
   - type: "python"
     user: false
     packages:
@@ -233,11 +239,11 @@ 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: "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
+  git_commit: "2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -257,7 +263,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   organization: "vsh"
   links:
     repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

target/nextflow/convert/from_xenium_to_h5mu/main.nf

@@ -1,4 +1,4 @@
-// from_xenium_to_h5mu v0.1.0
+// from_xenium_to_h5mu v0.1.1
 // 
 // 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
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "from_xenium_to_h5mu",
   "namespace" : "convert",
-  "version" : "v0.1.0",
+  "version" : "v0.1.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3162,6 +3162,10 @@ meta = [
       "type" : "file",
       "path" : "/src/utils/setup_logger.py"
     },
+    {
+      "type" : "file",
+      "path" : "/src/utils/unzip_archived_folder.py"
+    },
     {
       "type" : "file",
       "path" : "/src/workflows/utils/labels.config",
@@ -3284,7 +3288,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.1.0",
+      "target_tag" : "v0.1.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3310,6 +3314,13 @@ meta = [
         }
       ],
       "test_setup" : [
+        {
+          "type" : "apt",
+          "packages" : [
+            "zip"
+          ],
+          "interactive" : false
+        },
         {
           "type" : "python",
           "user" : false,
@@ -3331,12 +3342,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_h5mu",
     "viash_version" : "0.9.4",
-    "git_commit" : "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36",
+    "git_commit" : "2baba3fff0930478c26da7e1bd99b29ee5dd83b3",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
     "name" : "openpipeline_spatial",
-    "version" : "v0.1.0",
+    "version" : "v0.1.1",
     "info" : {
       "test_resources" : [
         {
@@ -3361,7 +3372,7 @@ meta = [
       ".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 := 'v0.1.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
     ],
     "organization" : "vsh",
     "links" : {
@@ -3386,7 +3397,9 @@ from pathlib import Path
 import scanpy as sc
 import pandas as pd
 import mudata as mu
+import zipfile
 import json
+import os
 
 ## VIASH START
 # The following code has been auto-generated by Viash.
@@ -3426,22 +3439,47 @@ dep = {
 
 sys.path.append(meta["resources_dir"])
 from setup_logger import setup_logger
+from unzip_archived_folder import extract_selected_files_from_zip
 
 logger = setup_logger()
 
+
+def _retrieve_input_data(xenium_output_bundle):
     # 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",
+
+    required_file_patterns = {
+        "count_matrix": "**/cell_feature_matrix.h5",
+        "cells_metadata": "**/cells.parquet",
+        "experiment": "**/experiment.xenium",
+        "metrics_summary": "**/metrics_summary.csv",
     }
 
+    if zipfile.is_zipfile(xenium_output_bundle):
+        xenium_output_bundle = extract_selected_files_from_zip(
+            xenium_output_bundle,
+            members=[pattern for pattern in required_file_patterns.values()],
+        )
+    else:
+        xenium_output_bundle = Path(xenium_output_bundle)
+
+    assert os.path.isdir(xenium_output_bundle), (
+        "Input is expected to be a (compressed) directory."
+    )
+
+    input_data = {}
+    for key, pattern in required_file_patterns.items():
+        file = list(xenium_output_bundle.glob(pattern))
+        assert len(file) == 1, (
+            f"Expected exactly one file matching pattern {pattern}, found {len(file)}."
+        )
+        input_data[key] = file[0]
+
+    return input_data
+
 
 def _format_cell_id_column(cell_id_column: pd.Series) -> pd.Series:
     """Convert cell IDs to string format, decoding bytes if necessary."""
@@ -3453,9 +3491,7 @@ def _format_cell_id_column(cell_id_column: pd.Series) -> pd.Series:
 # 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()}."
-)
+input_data = _retrieve_input_data(par["input"])
 
 adata = sc.read_10x_h5(input_data["count_matrix"])
 metadata = pd.read_parquet(input_data["cells_metadata"], engine="pyarrow")
@@ -3862,7 +3898,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline_spatial/convert/from_xenium_to_h5mu",
-    "tag" : "v0.1.0"
+    "tag" : "v0.1.1"
   },
   "label" : [
     "lowmem",

target/nextflow/convert/from_xenium_to_h5mu/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'convert/from_xenium_to_h5mu'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = 'v0.1.1'
   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'
 }

target/nextflow/convert/from_xenium_to_h5mu/unzip_archived_folder.py

@@ -0,0 +1,50 @@
+import fnmatch
+import zipfile
+import tempfile
+from pathlib import Path
+from typing import Union
+
+
+def unzip_archived_folder(archived_folder: Union[str, Path]) -> Union[str, Path]:
+    """
+    Extracts a ZIP archive to a temporary directory and returns the path to the extracted folder.
+
+    Args:
+        zip_path (Union[str, Path]): Path to the ZIP archive.
+
+    Returns:
+        extracted_path (Union[str, Path]): Path to the extracted folder inside the temporary directory.
+    """
+
+    temp_dir = Path(tempfile.TemporaryDirectory().name)
+    with zipfile.ZipFile(archived_folder, "r") as archive:
+        archive.extractall(temp_dir)
+
+    return temp_dir / Path(archived_folder).stem
+
+
+def extract_selected_files_from_zip(
+    zip_path: Union[str, Path], members: list[Union[str, Path]]
+) -> Union[str, Path]:
+    """
+    Extracts selected files (supports glob patterns) from a ZIP archive to a temporary directory.
+
+    Args:
+        zip_path (Union[str, Path]): Path to the ZIP archive.
+        members (list[str]): List of file paths within the archive to extract.
+
+    Returns:
+        Path: Path to the extraction directory.
+    """
+
+    temp_dir = Path(tempfile.TemporaryDirectory().name)
+
+    with zipfile.ZipFile(zip_path, "r") as archive:
+        all_files = archive.namelist()
+        selected = set()
+        for pattern in members:
+            selected.update(fnmatch.filter(all_files, str(pattern)))
+        for member in selected:
+            archive.extract(member, temp_dir)
+
+    return temp_dir

target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "from_xenium_to_spatialdata"
 namespace: "convert"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -173,6 +173,8 @@ resources:
   is_executable: true
 - type: "file"
   path: "setup_logger.py"
+- type: "file"
+  path: "unzip_archived_folder.py"
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
@@ -278,7 +280,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -303,6 +305,10 @@ engines:
     github:
     - "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
     upgrade: true
+  - type: "apt"
+    packages:
+    - "zip"
+    interactive: false
   entrypoint: []
   cmd: null
 - type: "native"
@@ -314,11 +320,11 @@ 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: "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
+  git_commit: "2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -338,7 +344,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   organization: "vsh"
   links:
     repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

target/nextflow/convert/from_xenium_to_spatialdata/main.nf

@@ -1,4 +1,4 @@
-// from_xenium_to_spatialdata v0.1.0
+// from_xenium_to_spatialdata v0.1.1
 // 
 // 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
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "from_xenium_to_spatialdata",
   "namespace" : "convert",
-  "version" : "v0.1.0",
+  "version" : "v0.1.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3251,6 +3251,10 @@ meta = [
       "type" : "file",
       "path" : "/src/utils/setup_logger.py"
     },
+    {
+      "type" : "file",
+      "path" : "/src/utils/unzip_archived_folder.py"
+    },
     {
       "type" : "file",
       "path" : "/src/workflows/utils/labels.config",
@@ -3373,7 +3377,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.1.0",
+      "target_tag" : "v0.1.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3411,6 +3415,13 @@ meta = [
             "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
           ],
           "upgrade" : true
+        },
+        {
+          "type" : "apt",
+          "packages" : [
+            "zip"
+          ],
+          "interactive" : false
         }
       ]
     },
@@ -3425,12 +3436,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialdata",
     "viash_version" : "0.9.4",
-    "git_commit" : "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36",
+    "git_commit" : "2baba3fff0930478c26da7e1bd99b29ee5dd83b3",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
     "name" : "openpipeline_spatial",
-    "version" : "v0.1.0",
+    "version" : "v0.1.1",
     "info" : {
       "test_resources" : [
         {
@@ -3455,7 +3466,7 @@ meta = [
       ".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 := 'v0.1.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
     ],
     "organization" : "vsh",
     "links" : {
@@ -3477,6 +3488,8 @@ tempscript=".viash_script.py"
 cat > "$tempscript" << VIASHMAIN
 import sys
 from spatialdata_io import xenium
+import zipfile
+from pathlib import Path
 
 ## VIASH START
 # The following code has been auto-generated by Viash.
@@ -3523,12 +3536,29 @@ dep = {
 
 sys.path.append(meta["resources_dir"])
 from setup_logger import setup_logger
+from unzip_archived_folder import unzip_archived_folder
 
 logger = setup_logger()
 
 logger.info("Reading in Xenium data...")
+
+if zipfile.is_zipfile(par["input"]):
+    required_file_patterns = [
+        "**/experiment.xenium",
+        "**/nucleus_boundaries.parquet",
+        "**/cell_boundaries.parquet",
+        "**/transcripts.parquet",
+        "**/cell_feature_matrix.h5",
+        "**/cells.parquet",
+        "**/morphology_mip.ome.tif",
+        "**/morphology_focus.ome.tif",
+    ]
+    xenium_output_bundle = unzip_archived_folder(par["input"])
+else:
+    xenium_output_bundle = Path(par["input"])
+
 sdata = xenium(
-    par["input"],
+    xenium_output_bundle,
     cells_boundaries=par["cells_boundaries"],
     nucleus_boundaries=par["nucleus_boundaries"],
     cells_as_circles=par["cells_as_circles"],
@@ -3927,7 +3957,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline_spatial/convert/from_xenium_to_spatialdata",
-    "tag" : "v0.1.0"
+    "tag" : "v0.1.1"
   },
   "label" : [
     "lowmem",

target/nextflow/convert/from_xenium_to_spatialdata/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'convert/from_xenium_to_spatialdata'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = 'v0.1.1'
   description = 'Converts the output from 10X Genomics Xenium dataset into a SpatialData objcet.\nBy default, the following files will be converted:\n  - `experiment.xenium`: File containing specifications.\n  - `nucleus_boundaries.parquet`: Polygons of nucleus boundaries.\n  - `cell_boundaries.parquet`: Polygons of cell boundaries.\n  - `transcripts.parquet`: File containing transcripts.\n  - `cell_feature_matrix.h5`: File containing cell feature matrix.\n  - `cells.parquet`: File containing cell metadata.\n  - `morphology_mip.ome.tif`: File containing morphology mip.\n  - `morphology_focus.ome.tif`: File containing morphology focus.\n  \n'
   author = 'Dorien Roosen, Weiwei Schultz'
 }

target/nextflow/convert/from_xenium_to_spatialdata/unzip_archived_folder.py

@@ -0,0 +1,50 @@
+import fnmatch
+import zipfile
+import tempfile
+from pathlib import Path
+from typing import Union
+
+
+def unzip_archived_folder(archived_folder: Union[str, Path]) -> Union[str, Path]:
+    """
+    Extracts a ZIP archive to a temporary directory and returns the path to the extracted folder.
+
+    Args:
+        zip_path (Union[str, Path]): Path to the ZIP archive.
+
+    Returns:
+        extracted_path (Union[str, Path]): Path to the extracted folder inside the temporary directory.
+    """
+
+    temp_dir = Path(tempfile.TemporaryDirectory().name)
+    with zipfile.ZipFile(archived_folder, "r") as archive:
+        archive.extractall(temp_dir)
+
+    return temp_dir / Path(archived_folder).stem
+
+
+def extract_selected_files_from_zip(
+    zip_path: Union[str, Path], members: list[Union[str, Path]]
+) -> Union[str, Path]:
+    """
+    Extracts selected files (supports glob patterns) from a ZIP archive to a temporary directory.
+
+    Args:
+        zip_path (Union[str, Path]): Path to the ZIP archive.
+        members (list[str]): List of file paths within the archive to extract.
+
+    Returns:
+        Path: Path to the extraction directory.
+    """
+
+    temp_dir = Path(tempfile.TemporaryDirectory().name)
+
+    with zipfile.ZipFile(zip_path, "r") as archive:
+        all_files = archive.namelist()
+        selected = set()
+        for pattern in members:
+            selected.update(fnmatch.filter(all_files, str(pattern)))
+        for member in selected:
+            archive.extract(member, temp_dir)
+
+    return temp_dir

target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "from_xenium_to_spatialexperiment"
 namespace: "convert"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -88,6 +88,8 @@ resources:
 - type: "r_script"
   path: "script.R"
   is_executable: true
+- type: "file"
+  path: "unzip_archived_folder.R"
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
@@ -192,7 +194,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -222,11 +224,11 @@ 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: "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
+  git_commit: "2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -246,7 +248,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   organization: "vsh"
   links:
     repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf

@@ -1,4 +1,4 @@
-// from_xenium_to_spatialexperiment v0.1.0
+// from_xenium_to_spatialexperiment v0.1.1
 // 
 // 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
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "from_xenium_to_spatialexperiment",
   "namespace" : "convert",
-  "version" : "v0.1.0",
+  "version" : "v0.1.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3147,6 +3147,10 @@ meta = [
       "path" : "script.R",
       "is_executable" : true
     },
+    {
+      "type" : "file",
+      "path" : "/src/utils/unzip_archived_folder.R"
+    },
     {
       "type" : "file",
       "path" : "/src/workflows/utils/labels.config",
@@ -3269,7 +3273,7 @@ meta = [
       "id" : "docker",
       "image" : "rocker/r2u:24.04",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.1.0",
+      "target_tag" : "v0.1.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3311,12 +3315,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialexperiment",
     "viash_version" : "0.9.4",
-    "git_commit" : "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36",
+    "git_commit" : "2baba3fff0930478c26da7e1bd99b29ee5dd83b3",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
     "name" : "openpipeline_spatial",
-    "version" : "v0.1.0",
+    "version" : "v0.1.1",
     "info" : {
       "test_resources" : [
         {
@@ -3341,7 +3345,7 @@ meta = [
       ".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 := 'v0.1.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
     ],
     "organization" : "vsh",
     "links" : {
@@ -3406,9 +3410,30 @@ rm(.viash_orig_warn)
 
 ### VIASH END
 
+source(paste0(meta\\$resources_dir, "/unzip_archived_folder.R"))
 
+cat("Reading input data...")
+if (tools::file_ext(par\\$input) == "zip") {
+  required_file_patterns <- c(
+    "**/cell_feature_matrix.h5",
+    "**/*.parquet",
+    "**/experiment.xenium"
+  )
+  tmp_dir <- extract_selected_files(
+    par\\$input,
+    members = required_file_patterns
+  )
+  xenium_output_bundle <- file.path(
+    tmp_dir,
+    tools::file_path_sans_ext(basename(par\\$input))
+  )
+} else {
+  xenium_output_bundle <- par\\$input
+}
+
+cat("Converting to SpatialExperiment")
 spe <- readXeniumSXE(
-  dirName = par\\$input,
+  dirName = xenium_output_bundle,
   returnType = "SPE",
   countMatPattern = "cell_feature_matrix.h5",
   metaDataPattern = "cells.parquet",
@@ -3418,6 +3443,7 @@ spe <- readXeniumSXE(
   altExps = par\\$alternative_experiment_features
 )
 
+cat("Saving output...")
 saveRDS(spe, file = par\\$output)
 VIASHMAIN
 Rscript "$tempscript"
@@ -3801,7 +3827,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline_spatial/convert/from_xenium_to_spatialexperiment",
-    "tag" : "v0.1.0"
+    "tag" : "v0.1.1"
   },
   "label" : [
     "lowmem",

target/nextflow/convert/from_xenium_to_spatialexperiment/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'convert/from_xenium_to_spatialexperiment'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = 'v0.1.1'
   description = 'Creates a SpatialExperiment object from the downloaded unzipped Xenium Output Bundle directory\nfor 10x Genomics Xenium spatial gene expression data, and saves it as a SpatialExperiment object.\nThe constructor assumes the downloaded unzipped Xenium Output Bundle has the following structure:\n\nMandatory files\n· | — cell_feature_matrix.h5\n· | — cells.parquet\nOptional files, by default added to the metadata() as a list of paths (will be converted to parquet):\n· | — transcripts.parquet\n· | — cell_boundaries.parquet\n· | — nucleus_boundaries.parquet\n· | — experiment.xenium\n'
   author = 'Dorien Roosen'
 }

target/nextflow/convert/from_xenium_to_spatialexperiment/unzip_archived_folder.R

@@ -0,0 +1,22 @@
+extract_selected_files <- function(zip_path, members) {
+  # Create a temporary directory for extraction
+  temp_dir <- tempfile("unzip_dir_")
+  dir.create(temp_dir)
+
+  # List all files in the archive
+  all_files <- utils::unzip(zip_path, list = TRUE)$Name
+
+  # Find files matching any of the glob patterns in 'members'
+  selected <- unique(unlist(
+    lapply(members, function(pattern) {
+      regex <- glob2rx(pattern)
+      grep(regex, all_files, value = TRUE)
+    })
+  ))
+
+  # Extract only the selected files
+  utils::unzip(zip_path, files = selected, exdir = temp_dir)
+
+  # Return the path to the extracted folder
+  file.path(temp_dir)
+}

target/nextflow/filter/subset_cosmx/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "subset_cosmx"
 namespace: "filter"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -191,7 +191,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -227,11 +227,11 @@ build_info:
   output: "target/nextflow/filter/subset_cosmx"
   executable: "target/nextflow/filter/subset_cosmx/main.nf"
   viash_version: "0.9.4"
-  git_commit: "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
+  git_commit: "2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -251,7 +251,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   organization: "vsh"
   links:
     repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

target/nextflow/filter/subset_cosmx/main.nf

@@ -1,4 +1,4 @@
-// subset_cosmx v0.1.0
+// subset_cosmx v0.1.1
 // 
 // 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
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "subset_cosmx",
   "namespace" : "filter",
-  "version" : "v0.1.0",
+  "version" : "v0.1.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3281,7 +3281,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.1.0",
+      "target_tag" : "v0.1.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3333,12 +3333,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/filter/subset_cosmx",
     "viash_version" : "0.9.4",
-    "git_commit" : "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36",
+    "git_commit" : "2baba3fff0930478c26da7e1bd99b29ee5dd83b3",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
     "name" : "openpipeline_spatial",
-    "version" : "v0.1.0",
+    "version" : "v0.1.1",
     "info" : {
       "test_resources" : [
         {
@@ -3363,7 +3363,7 @@ meta = [
       ".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 := 'v0.1.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
     ],
     "organization" : "vsh",
     "links" : {
@@ -3858,7 +3858,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline_spatial/filter/subset_cosmx",
-    "tag" : "v0.1.0"
+    "tag" : "v0.1.1"
   },
   "label" : [
     "lowmem",

target/nextflow/filter/subset_cosmx/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'filter/subset_cosmx'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = 'v0.1.1'
   description = 'Filters the output from NanoString experiment to keep only a subset of the fields of view.\nExpected input folder structure:\npath/to/dataset/\n    ├── CellComposite/\n    ├── CellLabels/\n    ├── CellOverlay/\n    ├── CompartmentLabels/\n    ├── <dataset_id>_exprMat_file.csv\n    ├── <dataset_id>_fov_positions_file.csv\n    ├── <dataset_id>_metadata_file.csv\n    └── <dataset_id>_tx_file.csv  \n'
   author = 'Dorien Roosen, Weiwei Schultz'
 }

target/nextflow/mapping/spaceranger_count/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "spaceranger_count"
 namespace: "mapping"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Jakub Majercik"
   roles:
@@ -408,7 +408,7 @@ engines:
   id: "docker"
   image: "ghcr.io/data-intuitive/spaceranger:3.1"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -426,11 +426,11 @@ build_info:
   output: "target/nextflow/mapping/spaceranger_count"
   executable: "target/nextflow/mapping/spaceranger_count/main.nf"
   viash_version: "0.9.4"
-  git_commit: "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
+  git_commit: "2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -450,7 +450,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   organization: "vsh"
   links:
     repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

target/nextflow/mapping/spaceranger_count/main.nf

@@ -1,4 +1,4 @@
-// spaceranger_count v0.1.0
+// spaceranger_count v0.1.1
 // 
 // 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
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "spaceranger_count",
   "namespace" : "mapping",
-  "version" : "v0.1.0",
+  "version" : "v0.1.1",
   "authors" : [
     {
       "name" : "Jakub Majercik",
@@ -3526,7 +3526,7 @@ meta = [
       "id" : "docker",
       "image" : "ghcr.io/data-intuitive/spaceranger:3.1",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.1.0",
+      "target_tag" : "v0.1.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3548,12 +3548,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/mapping/spaceranger_count",
     "viash_version" : "0.9.4",
-    "git_commit" : "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36",
+    "git_commit" : "2baba3fff0930478c26da7e1bd99b29ee5dd83b3",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
     "name" : "openpipeline_spatial",
-    "version" : "v0.1.0",
+    "version" : "v0.1.1",
     "info" : {
       "test_resources" : [
         {
@@ -3578,7 +3578,7 @@ meta = [
       ".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 := 'v0.1.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
     ],
     "organization" : "vsh",
     "links" : {
@@ -4072,7 +4072,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline_spatial/mapping/spaceranger_count",
-    "tag" : "v0.1.0"
+    "tag" : "v0.1.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/mapping/spaceranger_count/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'mapping/spaceranger_count'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = 'v0.1.1'
   description = 'Count gene expression and protein expression reads from a single capture area.'
   author = 'Jakub Majercik'
 }

target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "spatial_process_samples"
 namespace: "workflows/multiomics"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -640,13 +640,13 @@ 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: "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
+  git_commit: "2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
   dependencies:
   - "target/dependencies/vsh/vsh/openpipeline/v3.0.0/nextflow/workflows/multiomics/process_samples"
 package_config:
   name: "openpipeline_spatial"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -666,7 +666,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   organization: "vsh"
   links:
     repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

target/nextflow/workflows/multiomics/spatial_process_samples/main.nf

@@ -1,4 +1,4 @@
-// spatial_process_samples v0.1.0
+// spatial_process_samples v0.1.1
 // 
 // 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
@@ -3037,7 +3037,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "spatial_process_samples",
   "namespace" : "workflows/multiomics",
-  "version" : "v0.1.0",
+  "version" : "v0.1.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3807,12 +3807,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/multiomics/spatial_process_samples",
     "viash_version" : "0.9.4",
-    "git_commit" : "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36",
+    "git_commit" : "2baba3fff0930478c26da7e1bd99b29ee5dd83b3",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
     "name" : "openpipeline_spatial",
-    "version" : "v0.1.0",
+    "version" : "v0.1.1",
     "info" : {
       "test_resources" : [
         {
@@ -3837,7 +3837,7 @@ meta = [
       ".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 := 'v0.1.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
     ],
     "organization" : "vsh",
     "links" : {

target/nextflow/workflows/multiomics/spatial_process_samples/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/multiomics/spatial_process_samples'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = 'v0.1.1'
   description = 'A pipeline to pre-process multiple spatial omics samples.'
   author = 'Dries Schaumont, Dorien Roosen, Weiwei Schultz'
 }

target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "spatial_qc"
 namespace: "workflows/qc"
-version: "v0.1.0"
+version: "v0.1.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -387,13 +387,13 @@ 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: "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36"
+  git_commit: "2baba3fff0930478c26da7e1bd99b29ee5dd83b3"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
   dependencies:
   - "target/dependencies/vsh/vsh/openpipeline/v3.0.0/nextflow/workflows/qc/qc"
 package_config:
   name: "openpipeline_spatial"
-  version: "v0.1.0"
+  version: "v0.1.1"
   info:
     test_resources:
     - type: "s3"
@@ -413,7 +413,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
   organization: "vsh"
   links:
     repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

target/nextflow/workflows/qc/spatial_qc/main.nf

@@ -1,4 +1,4 @@
-// spatial_qc v0.1.0
+// spatial_qc v0.1.1
 // 
 // 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
@@ -3037,7 +3037,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "spatial_qc",
   "namespace" : "workflows/qc",
-  "version" : "v0.1.0",
+  "version" : "v0.1.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3505,12 +3505,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/qc/spatial_qc",
     "viash_version" : "0.9.4",
-    "git_commit" : "3f8c1506dc59a8c9bb2a3fa6acb40e4e40291e36",
+    "git_commit" : "2baba3fff0930478c26da7e1bd99b29ee5dd83b3",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
     "name" : "openpipeline_spatial",
-    "version" : "v0.1.0",
+    "version" : "v0.1.1",
     "info" : {
       "test_resources" : [
         {
@@ -3535,7 +3535,7 @@ meta = [
       ".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 := 'v0.1.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
     ],
     "organization" : "vsh",
     "links" : {

target/nextflow/workflows/qc/spatial_qc/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/qc/spatial_qc'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.1.0'
+  version = 'v0.1.1'
   description = 'A pipeline to add basic qc statistics to a MuData containing spatial data.'
   author = 'Dries Schaumont, Dorien Roosen, Weiwei Schultz'
 }