Build branch build/main with version build_main (798a0cb)

Build pipeline: openpipelines-bio.openpipeline-spatial.build-main-7frxn Source commit: 798a0cb269 Source message: deploy: 5fc3bcd8432928c148e8f27d6ae49214a91add67
2025-08-22 15:00:12 +00:00
parent 8c9abfcde2
commit 5273fbdd05
52 changed files with 6860 additions and 49 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,3 +17,5 @@
 * `workflows/qc/qc`: Added a pipeline for calculating qc metrics of spatial omics samples (PR #5).

 * `workflows/multiomics/spatial_process_samples`: Added a pipeline to pre-process multiple spatial omics samples (PR #7).
+
+* `convert/from_h5mu_to_spatialexperiment`: Added converter component for H5MU data to SpatialExperiment objects (PR #15).
--- a/src/convert/from_h5mu_to_spatialexperiment/config.vsh.yaml
+++ b/src/convert/from_h5mu_to_spatialexperiment/config.vsh.yaml
@@ -0,0 +1,75 @@
+name: "from_h5mu_to_spatialexperiment"
+namespace: "convert"
+scope: "public"
+description: |
+  Converts an h5mu file into a SpatialExperiment object.
+authors:
+  - __merge__: /src/authors/dorien_roosen.yaml
+    roles: [ author ]
+arguments:
+  - name: "--input"
+    alternatives: ["-i"]
+    type: file
+    description: Input h5mu file
+    direction: input
+    required: true
+    example: input.h5mu
+  - name: "--modality"
+    type: string
+    required: true
+    default: "rna"
+    description: Name of the modality to be converted.
+  - name: "--obsm_spatial_coordinates"
+    type: string
+    required: false
+    description: |
+      Key in the .obsm field that contains the spatial coordinates. 
+      Will be mapped to spatialCoords in the SpatialExperiment object.
+  - name: "--output"
+    alternatives: ["-o"]
+    type: file
+    description: Output SpatialExperiment file
+    direction: output
+    required: true
+    example: output.rds
+resources:
+  - type: r_script
+    path: script.R
+test_resources:
+  - type: r_script
+    path: test.R
+  - path: /resources_test/aviti/aviti_teton_tiny.h5mu
+  - path: /resources_test/cosmx/Lung5_Rep2_tiny.h5mu
+  - path: /resources_test/xenium/xenium_tiny.h5mu
+
+engines:
+  - type: docker
+    image: rocker/r2u:22.04
+    setup:
+      - type: apt
+        packages: 
+          - libhdf5-dev
+          - libgeos-dev
+      - type: r
+        cran: [ hdf5r, SpatialExperiment ]
+        github: scverse/anndataR@36f3caad9a7f360165c1510bbe0c62657580415a
+    test_setup:
+      - type: docker
+        env: 
+          - RETICULATE_PYTHON=/usr/bin/python
+      - type: apt
+        packages:
+          - python3
+          - python3-pip
+          - python3-dev
+          - python-is-python3
+      - type: r
+        cran: [ reticulate, testthat ]
+      - type: python
+        __merge__: /src/base/requirements/anndata_mudata.yaml
+
+runners:
+  - type: executable
+  - type: nextflow
+    directives:
+      label: [lowmem, singlecpu]
--- a/src/convert/from_h5mu_to_spatialexperiment/script.R
+++ b/src/convert/from_h5mu_to_spatialexperiment/script.R
@@ -0,0 +1,113 @@
+library(SpatialExperiment)
+library(SingleCellExperiment)
+library(hdf5r)
+library(Matrix)
+library(hdf5r)
+
+## VIASH START
+par <- list(
+  input = "resources_test/xenium/xenium_tiny.h5mu",
+  output = "xenium_test.rds",
+  modality = "rna",
+  obsm_spatial_coordinates = "spatial"
+)
+## VIASH END
+
+
+h5mu_to_h5ad <- function(h5mu_path, modality_name) {
+  tmp_path <- tempfile(fileext = ".h5ad")
+  mod_location <- paste("mod", modality_name, sep = "/")
+  h5src <- hdf5r::H5File$new(h5mu_path, "r")
+  h5dest <- hdf5r::H5File$new(tmp_path, "w")
+  # Copy over the child objects and the child attributes from root
+  # Root cannot be copied directly because it always exists and
+  # copying does not allow overwriting.
+  children <- hdf5r::list.objects(h5src,
+    path = mod_location,
+    full.names = FALSE, recursive = FALSE
+  )
+  for (child in children) {
+    h5dest$obj_copy_from(
+      h5src, paste(mod_location, child, sep = "/"),
+      paste0("/", child)
+    )
+  }
+  # Also copy the root attributes
+  root_attrs <- hdf5r::h5attr_names(x = h5src)
+  for (attr in root_attrs) {
+    h5a <- h5src$attr_open(attr_name = attr)
+    robj <- h5a$read()
+    h5dest$create_attr_by_name(
+      attr_name = attr,
+      obj_name = ".",
+      robj = robj,
+      space = h5a$get_space(),
+      dtype = h5a$get_type()
+    )
+  }
+  h5src$close()
+  h5dest$close()
+
+  tmp_path
+}
+
+read_spatial_coordinates <- function(sce, spatial_coordinates_name) {
+  # Check if the specified spatial coordinates exist in reducedDims
+  reduced_dims <- SingleCellExperiment::reducedDims(sce)
+  if (par$obsm_spatial_coordinates %in% names(reduced_dims)) {
+    spatial_coords <- reduced_dims[[par$obsm_spatial_coordinates]]
+    if (ncol(spatial_coords) != 2) {
+      stop(
+        "Spatial coordinates must have 2 columns, but found ",
+        ncol(spatial_coords), " columns"
+      )
+    }
+    # Set proper column names for spatial coordinates
+    colnames(spatial_coords) <- c("x", "y")
+  } else {
+    warning(
+      "Spatial coordinates '", par$obsm_spatial_coordinates,
+      "' not found in reducedDims. Available dimensions: ",
+      paste(names(reduced_dims), collapse = ", ")
+    )
+    spatial_coords <- NULL
+  }
+  spatial_coords
+}
+
+main <- function() {
+  # Convert to AnnData
+  cat("Converting H5MU file to H5AD...\n")
+  h5file <- h5mu_to_h5ad(par$input, par$modality)
+
+  # Convert to SpatialExperiment
+  cat("Converting to SingleCellExperiment...\n")
+  sce <- anndataR::read_h5ad(h5file, as = "SingleCellExperiment")
+
+  # Extract spatial coordinates if specified
+  if (
+    !is.null(par$obsm_spatial_coordinates) &&
+      length(par$obsm_spatial_coordinates) > 0
+  ) {
+    cat("Reading in spatial coordinates...\n")
+    spatial_coords <- read_spatial_coordinates(
+      sce, par$obsm_spatial_coordinates
+    )
+    SingleCellExperiment::reducedDims(sce)[[
+      par$obsm_spatial_coordinates
+    ]] <- NULL
+  } else {
+    spatial_coords <- NULL
+  }
+
+  # Converting SingleCellExperiment to SpatialExperiment
+  cat("Converting to SpatialExperiment...\n")
+  spe <- as(sce, "SpatialExperiment")
+  SpatialExperiment::spatialCoords(spe) <- spatial_coords
+
+  # Saving SpatialExperiment object
+  cat("Saving SpatialExperiment object to:", par$output, "\n")
+  saveRDS(spe, file = par$output, compress = FALSE)
+}
+
+main()
--- a/src/convert/from_h5mu_to_spatialexperiment/test.R
+++ b/src/convert/from_h5mu_to_spatialexperiment/test.R
@@ -0,0 +1,475 @@
+library(testthat)
+library(SpatialExperiment)
+library(SingleCellExperiment)
+library(hdf5r)
+library(Matrix)
+library(reticulate)
+
+mu <- reticulate::import("mudata")
+ad <- reticulate::import("anndata")
+
+## VIASH START
+meta <- list(
+  resources_dir = "resources_test"
+)
+## VIASH END
+
+# Helper function to create mock H5MU test data
+create_mock_h5mu <- function(path) {
+  n_obs <- 5
+  n_var_mod1 <- 4
+  n_var_mod2 <- 3
+
+  # ============== MOD1 MODALITY ==============
+
+  mod1_x_data <- matrix(c(
+    1, 2, 3, 0,
+    4, 5, 6, 2,
+    0, 1, 2, 3,
+    2, 0, 1, 4,
+    1, 3, 0, 2
+  ), nrow = n_obs, ncol = n_var_mod1, byrow = TRUE)
+
+
+  # Create obs dataframe
+  mod1_obs <- data.frame(
+    Obs1 = c("A", "B", "A", "C", "B"),
+    Obs2 = c(0.9, 0.8, 0.95, 0.7, 0.85),
+    Obs3 = c(FALSE, FALSE, TRUE, FALSE, FALSE),
+    row.names = paste0("cell_", 1:n_obs),
+    stringsAsFactors = FALSE
+  )
+  # Create var dataframe
+  mod1_var <- data.frame(
+    Feat1 = c("A", "B", "C", "D"),
+    Feat2 = c(TRUE, FALSE, TRUE, FALSE),
+    Feat3 = c(1.6, 2.2, 1.2, 1.8),
+    row.names = paste0("gene_", 1:n_var_mod1),
+    stringsAsFactors = FALSE
+  )
+
+  # Create layers
+  mod1_layers <- list(
+    counts = mod1_x_data * 2
+  )
+
+  # Create obsm
+  obsm_1 <- matrix(c(
+    100.5, 200.3,
+    150.2, 180.7,
+    120.8, 220.1,
+    180.4, 160.9,
+    200.1, 190.5
+  ), nrow = n_obs, ncol = 2, byrow = TRUE)
+
+  obsm_2 <- matrix(c(
+    -1.2, 0.8, 0.3,
+    1.1, -0.5, -0.2,
+    0.3, 1.2, 0.7,
+    -0.8, -0.3, 1.1,
+    0.9, 0.2, -0.9
+  ), nrow = n_obs, ncol = 3, byrow = TRUE)
+
+  mod1_obsm <- list(
+    Obsm1 = obsm_1,
+    Obsm2 = obsm_2
+  )
+
+  # Create uns (unstructured metadata)
+  mod1_uns <- list(
+    experiment_info = "metadata"
+  )
+
+  # Create AnnData object for mod1 using AnnDataR
+  ad_mod1 <- ad$AnnData(
+    X = mod1_x_data,
+    obs = mod1_obs,
+    var = mod1_var,
+    layers = mod1_layers,
+    obsm = mod1_obsm,
+    uns = mod1_uns
+  )
+
+  # ============== MOD2 MODALITY ==============
+
+  # Create expression matrix
+  mod2_x_data <- matrix(c(
+    10, 20, 15,
+    25, 30, 18,
+    12, 22, 20,
+    18, 25, 12,
+    20, 28, 16
+  ), nrow = n_obs, ncol = n_var_mod2, byrow = TRUE)
+
+  # Create obs dataframe
+  mod2_obs <- data.frame(
+    Obs = c("C", "D", "C", "E", "D"),
+    row.names = paste0("cell_", 1:n_obs),
+    stringsAsFactors = FALSE
+  )
+
+  # Create var dataframe
+  mod2_var <- data.frame(
+    Feat = c("d", "e", "g"),
+    row.names = paste0("protein_", 1:n_var_mod2),
+    stringsAsFactors = FALSE
+  )
+
+  # Create AnnData object for mod2
+  ad_mod2 <- ad$AnnData(
+    X = mod2_x_data,
+    obs = mod2_obs,
+    var = mod2_var
+  )
+
+  # ============== CREATE MUDATA ==============
+
+  # Create MuData object using reticulate
+  mdata <- mu$MuData(list(
+    mod1 = ad_mod1,
+    mod2 = ad_mod2
+  ))
+
+  # Write Mudata to path
+  mdata$write_h5mu(path)
+  path
+}
+
+# Main test
+test_simple_execution <- function() {
+  cat("> > Testing Simple Conversion\n")
+  cat("> Creating mock H5MU file\n")
+
+  # Create mock H5MU file
+  test_h5mu <- tempfile(fileext = ".h5mu")
+  create_mock_h5mu(test_h5mu)
+
+  # Output file
+  out_rds <- tempfile(fileext = ".rds")
+
+  # Run conversion
+  cat("> Running conversion\n")
+  out <- processx::run(
+    meta[["executable"]],
+    c(
+      "--input", test_h5mu,
+      "--modality", "mod1",
+      "--output", out_rds,
+      "--obsm_spatial_coordinates", "Obsm1"
+    )
+  )
+
+  cat("> Checking execution status\n")
+  testthat::expect_equal(out$status, 0)
+  testthat::expect_true(file.exists(out_rds))
+
+  cat("> Reading output file\n")
+  spe <- readRDS(file = out_rds)
+  testthat::expect_s4_class(spe, "SpatialExperiment")
+
+  cat("> Opening input file for comparison\n")
+  mod1 <- mu$read_h5ad(test_h5mu, mod = "mod1")
+
+  cat("> Testing dimensions\n")
+  dim_spe <- dim(spe)
+  dim_h5mu <- dim(mod1$X)
+
+  testthat::expect_equal(dim_spe[1], dim_h5mu[2])
+  testthat::expect_equal(dim_spe[2], dim_h5mu[1])
+  testthat::expect_equal(nrow(spe), 4)
+  testthat::expect_equal(ncol(spe), 5)
+
+  cat("> Testing colData (obs) transfer and data types\n")
+  col_data <- SummarizedExperiment::colData(spe)
+  coldata_cols <- colnames(col_data)
+  obs_cols <- colnames(mod1$obs)
+  testthat::expect_true(all(obs_cols %in% coldata_cols))
+
+  # Test data types in colData
+  testthat::expect_true(is.factor(col_data$Obs1))
+  testthat::expect_true(is.numeric(col_data$Obs2))
+  testthat::expect_true(is.logical(col_data$Obs3))
+
+  cat("> Testing rowData (var) transfer and data types\n")
+  row_data <- SummarizedExperiment::rowData(spe)
+  row_names <- colnames(row_data)
+  var_cols <- colnames(mod1$var)
+  testthat::expect_true(all(var_cols %in% row_names))
+
+  # Test data types in rowData
+  testthat::expect_true(is.character(row_data$Feat1))
+  testthat::expect_true(is.logical(row_data$Feat2))
+  testthat::expect_true(is.numeric(row_data$Feat3))
+
+  cat("> Testing spatialCoords\n")
+  spatial_coords <- SpatialExperiment::spatialCoords(spe)
+  testthat::expect_false(is.null(spatial_coords))
+  testthat::expect_equal(ncol(spatial_coords), 2)
+  testthat::expect_equal(nrow(spatial_coords), ncol(spe))
+  testthat::expect_identical(colnames(spatial_coords), c("x", "y"))
+
+  # Test spatial coordinate data types and values
+  testthat::expect_true(is.numeric(spatial_coords[, "x"]))
+  testthat::expect_true(is.numeric(spatial_coords[, "y"]))
+
+  # Compare with original spatial coordinates
+  original_spatial <- mod1$obsm[["Obsm1"]]
+  testthat::expect_equal(
+    as.numeric(original_spatial),
+    as.numeric(spatial_coords)
+  )
+
+  cat("> Testing assay data\n")
+  counts_matrix <- SummarizedExperiment::assays(spe)[["counts"]]
+  testthat::expect_true(is(counts_matrix, "Matrix") || is.matrix(counts_matrix))
+  testthat::expect_true(all(counts_matrix >= 0))
+  testthat::expect_equal(dim(counts_matrix), c(4, 5))
+
+  cat("> Testing reducedDims\n")
+  # PCA should not be in reducedDims since we only specified spatial
+  red_dims <- SingleCellExperiment::reducedDims(spe)
+  testthat::expect_false(is.null(red_dims))
+  testthat::expect_equal(names(red_dims), c("Obsm2"))
+  testthat::expect_equal(dim(red_dims$Obsm2), c(5, 3))
+  testthat::expect_true(is.numeric(red_dims$Obsm2))
+
+  # Compare with original spatial coordinates
+  original_dimred <- mod1$obsm[["Obsm2"]]
+  testthat::expect_equal(
+    as.numeric(red_dims$Obsm2),
+    as.numeric(original_dimred)
+  )
+
+  # Clean up
+  unlink(c(test_h5mu, out_rds))
+}
+
+test_xenium_execution <- function() {
+  cat("> > Testing Xenium Conversion\n")
+  xenium_h5mu <- paste0(
+    meta[["resources_dir"]],
+    "/xenium_tiny.h5mu"
+  )
+
+  # Output file
+  out_rds <- tempfile(fileext = ".rds")
+
+  # Run conversion
+  cat("> Running conversion\n")
+  out <- processx::run(
+    meta[["executable"]],
+    c(
+      "--input", xenium_h5mu,
+      "--modality", "rna",
+      "--output", out_rds,
+      "--obsm_spatial_coordinates", "spatial"
+    )
+  )
+
+  cat("> Checking execution status\n")
+  testthat::expect_equal(out$status, 0)
+  testthat::expect_true(file.exists(out_rds))
+
+  cat("> Reading output file\n")
+  xenium_spe <- readRDS(file = out_rds)
+  testthat::expect_s4_class(xenium_spe, "SpatialExperiment")
+
+  cat("> Opening input file for comparison\n")
+  rna_mod <- mu$read_h5ad(xenium_h5mu, mod = "rna")
+
+  cat("> Testing dimensions\n")
+  dim_spe <- dim(xenium_spe)
+  dim_h5mu <- dim(rna_mod$X)
+
+  testthat::expect_equal(dim_spe[1], dim_h5mu[2])
+  testthat::expect_equal(dim_spe[2], dim_h5mu[1])
+
+  cat("> Testing colData (obs) transfer and data types\n")
+  col_data <- SummarizedExperiment::colData(xenium_spe)
+  coldata_cols <- colnames(col_data)
+  obs_cols <- colnames(rna_mod$obs)
+  testthat::expect_true(all(obs_cols %in% coldata_cols))
+
+  cat("> Testing rowData (var) transfer and data types\n")
+  row_data <- SummarizedExperiment::rowData(xenium_spe)
+  row_names <- colnames(row_data)
+  var_cols <- colnames(rna_mod$var)
+  testthat::expect_true(all(var_cols %in% row_names))
+
+  cat("> Testing spatialCoords\n")
+  spatial_coords <- SpatialExperiment::spatialCoords(xenium_spe)
+  testthat::expect_false(is.null(spatial_coords))
+  testthat::expect_equal(ncol(spatial_coords), 2)
+  testthat::expect_equal(nrow(spatial_coords), ncol(xenium_spe))
+  testthat::expect_identical(colnames(spatial_coords), c("x", "y"))
+
+  # Test spatial coordinate data types and values
+  testthat::expect_true(is.numeric(spatial_coords[, "x"]))
+  testthat::expect_true(is.numeric(spatial_coords[, "y"]))
+
+  # Compare with original spatial coordinates
+  original_spatial <- rna_mod$obsm[["spatial"]]
+  testthat::expect_equal(
+    as.numeric(original_spatial),
+    as.numeric(spatial_coords)
+  )
+
+  # Clean up
+  unlink(c(xenium_h5mu, out_rds))
+}
+
+test_aviti_execution <- function() {
+  cat("> > Testing Aviti Conversion\n")
+  aviti_h5mu <- paste0(
+    meta[["resources_dir"]],
+    "/aviti_teton_tiny.h5mu"
+  )
+
+  # Output file
+  out_rds <- tempfile(fileext = ".rds")
+
+  # Run conversion
+  cat("> Running conversion\n")
+  out <- processx::run(
+    meta[["executable"]],
+    c(
+      "--input", aviti_h5mu,
+      "--modality", "rna",
+      "--output", out_rds,
+      "--obsm_spatial_coordinates", "spatial"
+    )
+  )
+
+  cat("> Checking execution status\n")
+  testthat::expect_equal(out$status, 0)
+  testthat::expect_true(file.exists(out_rds))
+
+  cat("> Reading output file\n")
+  aviti_spe <- readRDS(file = out_rds)
+  testthat::expect_s4_class(aviti_spe, "SpatialExperiment")
+
+  cat("> Opening input file for comparison\n")
+  rna_mod <- mu$read_h5ad(aviti_h5mu, mod = "rna")
+
+  cat("> Testing dimensions\n")
+  dim_spe <- dim(aviti_spe)
+  dim_h5mu <- dim(rna_mod$X)
+
+  testthat::expect_equal(dim_spe[1], dim_h5mu[2])
+  testthat::expect_equal(dim_spe[2], dim_h5mu[1])
+
+  cat("> Testing colData (obs) transfer and data types\n")
+  col_data <- SummarizedExperiment::colData(aviti_spe)
+  coldata_cols <- colnames(col_data)
+  obs_cols <- colnames(rna_mod$obs)
+  testthat::expect_true(all(obs_cols %in% coldata_cols))
+
+  cat("> Testing rowData (var) transfer and data types\n")
+  row_data <- SummarizedExperiment::rowData(aviti_spe)
+  row_names <- colnames(row_data)
+  var_cols <- colnames(rna_mod$var)
+  testthat::expect_true(all(var_cols %in% row_names))
+
+  cat("> Testing spatialCoords\n")
+  spatial_coords <- SpatialExperiment::spatialCoords(aviti_spe)
+  testthat::expect_false(is.null(spatial_coords))
+  testthat::expect_equal(ncol(spatial_coords), 2)
+  testthat::expect_equal(nrow(spatial_coords), ncol(aviti_spe))
+  testthat::expect_identical(colnames(spatial_coords), c("x", "y"))
+
+  # Test spatial coordinate data types and values
+  testthat::expect_true(is.numeric(spatial_coords[, "x"]))
+  testthat::expect_true(is.numeric(spatial_coords[, "y"]))
+
+  # Compare with original spatial coordinates
+  original_spatial <- rna_mod$obsm[["spatial"]]
+  testthat::expect_equal(
+    as.numeric(original_spatial),
+    as.numeric(spatial_coords)
+  )
+
+  # Clean up
+  unlink(c(aviti_h5mu, out_rds))
+}
+
+test_cosmx_execution <- function() {
+  cat("> > Testing CosMx Conversion\n")
+  cosmx_h5mu <- paste0(
+    meta[["resources_dir"]],
+    "/Lung5_Rep2_tiny.h5mu"
+  )
+
+  # Output file
+  out_rds <- tempfile(fileext = ".rds")
+
+  # Run conversion
+  cat("> Running conversion\n")
+  out <- processx::run(
+    meta[["executable"]],
+    c(
+      "--input", cosmx_h5mu,
+      "--modality", "rna",
+      "--output", out_rds,
+      "--obsm_spatial_coordinates", "spatial"
+    )
+  )
+
+  cat("> Checking execution status\n")
+  testthat::expect_equal(out$status, 0)
+  testthat::expect_true(file.exists(out_rds))
+
+  cat("> Reading output file\n")
+  cosmx_spe <- readRDS(file = out_rds)
+  testthat::expect_s4_class(cosmx_spe, "SpatialExperiment")
+
+  cat("> Opening input file for comparison\n")
+  rna_mod <- mu$read_h5ad(cosmx_h5mu, mod = "rna")
+
+  cat("> Testing dimensions\n")
+  dim_spe <- dim(cosmx_spe)
+  dim_h5mu <- dim(rna_mod$X)
+
+  testthat::expect_equal(dim_spe[1], dim_h5mu[2])
+  testthat::expect_equal(dim_spe[2], dim_h5mu[1])
+
+  cat("> Testing colData (obs) transfer and data types\n")
+  col_data <- SummarizedExperiment::colData(cosmx_spe)
+  coldata_cols <- colnames(col_data)
+  obs_cols <- colnames(rna_mod$obs)
+  testthat::expect_true(all(obs_cols %in% coldata_cols))
+
+  cat("> Testing rowData (var) transfer and data types\n")
+  row_data <- SummarizedExperiment::rowData(cosmx_spe)
+  row_names <- colnames(row_data)
+  var_cols <- colnames(rna_mod$var)
+  testthat::expect_true(all(var_cols %in% row_names))
+
+  cat("> Testing spatialCoords\n")
+  spatial_coords <- SpatialExperiment::spatialCoords(cosmx_spe)
+  testthat::expect_false(is.null(spatial_coords))
+  testthat::expect_equal(ncol(spatial_coords), 2)
+  testthat::expect_equal(nrow(spatial_coords), ncol(cosmx_spe))
+  testthat::expect_identical(colnames(spatial_coords), c("x", "y"))
+
+  # Test spatial coordinate data types and values
+  testthat::expect_true(is.numeric(spatial_coords[, "x"]))
+  testthat::expect_true(is.numeric(spatial_coords[, "y"]))
+
+  # Compare with original spatial coordinates
+  original_spatial <- rna_mod$obsm[["spatial"]]
+  testthat::expect_equal(
+    as.numeric(original_spatial),
+    as.numeric(spatial_coords)
+  )
+
+  # Clean up
+  unlink(c(cosmx_h5mu, out_rds))
+}
+
+cat("Starting tests...")
+test_simple_execution()
+test_xenium_execution()
+test_aviti_execution()
+test_cosmx_execution()
+
+cat("All tests completed!\n")
--- a/target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml
@@ -290,7 +290,7 @@ build_info:
  output: "target/executable/convert/from_cells2stats_to_h5mu"
  executable: "target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu"
  viash_version: "0.9.4"
-  git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+  git_commit: "798a0cb2692eaac648662732a05bb48f951f36a0"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu
+++ b/target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_cells2stats_to_h5mu"
-LABEL org.opencontainers.image.created="2025-08-22T08:22:46Z"
+LABEL org.opencontainers.image.created="2025-08-22T14:30:50Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+LABEL org.opencontainers.image.revision="798a0cb2692eaac648662732a05bb48f951f36a0"
 LABEL org.opencontainers.image.version="build_main"

 VIASHDOCKER
--- a/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml
@@ -225,7 +225,7 @@ build_info:
  output: "target/executable/convert/from_cosmx_to_h5mu"
  executable: "target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu"
  viash_version: "0.9.4"
-  git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+  git_commit: "798a0cb2692eaac648662732a05bb48f951f36a0"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu
+++ b/target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu
@@ -459,9 +459,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_cosmx_to_h5mu"
-LABEL org.opencontainers.image.created="2025-08-22T08:22:48Z"
+LABEL org.opencontainers.image.created="2025-08-22T14:30:52Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+LABEL org.opencontainers.image.revision="798a0cb2692eaac648662732a05bb48f951f36a0"
 LABEL org.opencontainers.image.version="build_main"

 VIASHDOCKER
--- a/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml
+++ b/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml
@@ -232,7 +232,7 @@ build_info:
  output: "target/executable/convert/from_cosmx_to_spatialexperiment"
  executable: "target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment"
  viash_version: "0.9.4"
-  git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+  git_commit: "798a0cb2692eaac648662732a05bb48f951f36a0"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment
+++ b/target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment
@@ -457,9 +457,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("BiocManager", quietly

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_cosmx_to_spatialexperiment"
-LABEL org.opencontainers.image.created="2025-08-22T08:22:47Z"
+LABEL org.opencontainers.image.created="2025-08-22T14:30:51Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+LABEL org.opencontainers.image.revision="798a0cb2692eaac648662732a05bb48f951f36a0"
 LABEL org.opencontainers.image.version="build_main"

 VIASHDOCKER
--- a/target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml
+++ b/target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml
@@ -0,0 +1,255 @@
+name: "from_h5mu_to_spatialexperiment"
+namespace: "convert"
+version: "build_main"
+authors:
+- name: "Dorien Roosen"
+  roles:
+  - "author"
+  info:
+    role: "Core Team Member"
+    links:
+      email: "dorien@data-intuitive.com"
+      github: "dorien-er"
+      linkedin: "dorien-roosen"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
+argument_groups:
+- name: "Arguments"
+  arguments:
+  - type: "file"
+    name: "--input"
+    alternatives:
+    - "-i"
+    description: "Input h5mu file"
+    info: null
+    example:
+    - "input.h5mu"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--modality"
+    description: "Name of the modality to be converted."
+    info: null
+    default:
+    - "rna"
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--obsm_spatial_coordinates"
+    description: "Key in the .obsm field that contains the spatial coordinates. \n\
+      Will be mapped to spatialCoords in the SpatialExperiment object.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output"
+    alternatives:
+    - "-o"
+    description: "Output SpatialExperiment file"
+    info: null
+    example:
+    - "output.rds"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "r_script"
+  path: "script.R"
+  is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
+description: "Converts an h5mu file into a SpatialExperiment object.\n"
+test_resources:
+- type: "r_script"
+  path: "test.R"
+  is_executable: true
+- type: "file"
+  path: "aviti_teton_tiny.h5mu"
+- type: "file"
+  path: "Lung5_Rep2_tiny.h5mu"
+- type: "file"
+  path: "xenium_tiny.h5mu"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+repositories:
+- type: "github"
+  name: "openpipeline"
+  repo: "openpipelines-bio/openpipeline"
+  tag: "2.1.2"
+links:
+  repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
+  docker_registry: "ghcr.io"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    label:
+    - "lowmem"
+    - "singlecpu"
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "rocker/r2u:22.04"
+  target_registry: "images.viash-hub.com"
+  target_tag: "build_main"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "libhdf5-dev"
+    - "libgeos-dev"
+    interactive: false
+  - type: "r"
+    cran:
+    - "hdf5r"
+    - "SpatialExperiment"
+    github:
+    - "scverse/anndataR@36f3caad9a7f360165c1510bbe0c62657580415a"
+    bioc_force_install: false
+    warnings_as_errors: true
+  test_setup:
+  - type: "docker"
+    env:
+    - "RETICULATE_PYTHON=/usr/bin/python"
+  - type: "apt"
+    packages:
+    - "python3"
+    - "python3-pip"
+    - "python3-dev"
+    - "python-is-python3"
+    interactive: false
+  - type: "r"
+    cran:
+    - "reticulate"
+    - "testthat"
+    bioc_force_install: false
+    warnings_as_errors: true
+  - type: "python"
+    user: false
+    packages:
+    - "anndata~=0.11.1"
+    - "mudata~=0.3.1"
+    script:
+    - "exec(\"try:\\n  import awkward\\nexcept ModuleNotFoundError:\\n  exit(0)\\\
+      nelse:  exit(1)\")"
+    upgrade: true
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/convert/from_h5mu_to_spatialexperiment/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  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: "798a0cb2692eaac648662732a05bb48f951f36a0"
+  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
+package_config:
+  name: "openpipeline_spatial"
+  version: "build_main"
+  info:
+    test_resources:
+    - type: "s3"
+      path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
+      dest: "resources_test"
+  repositories:
+  - type: "github"
+    name: "openpipeline"
+    repo: "openpipelines-bio/openpipeline"
+    tag: "2.1.2"
+  viash_version: "0.9.4"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
+    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    )'"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'build_main'"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
+    docker_registry: "ghcr.io"
--- a/target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment
+++ b/target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment
--- a/target/executable/convert/from_h5mu_to_spatialexperiment/nextflow_labels.config
+++ b/target/executable/convert/from_h5mu_to_spatialexperiment/nextflow_labels.config
@@ -0,0 +1,68 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // CPU resources
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 4 }
+  withLabel: midcpu { cpus = 10 }
+  withLabel: highcpu { cpus = 20 }
+  
+  // Memory resources
+  withLabel: lowmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
+
+  // Disk space
+  // Nextflow apparently can't handle empty directives, i.e.
+  // withLabel: lowdisk {}
+  // so for that reason we have to add a dummy directive
+  withLabel: lowdisk {
+    dummyDirective = "dummyValue"
+  }
+  withLabel: middisk {
+    dummyDirective = "dummyValue"
+  }
+  withLabel: highdisk {
+    dummyDirective = "dummyValue"
+  }
+  withLabel: veryhighdisk {
+    dummyDirective = "dummyValue"
+  }
+  // NOTE: The above labels intentionally do not have an effect by default.
+  // The user should set the disk space requirements by adding the following
+  // to the compute environment:
+  //
+  // withLabel: lowdisk { disk = { 20.GB * task.attempt } }
+  // withLabel: middisk { disk = { 100.GB * task.attempt } }
+  // withLabel: highdisk { disk = { 200.GB * task.attempt } }
+  // withLabel: veryhighdisk { disk = { 500.GB * task.attempt } }
+}
+
+def get_memory(to_compare) {
+  if (!process.containsKey("maxMemory") || !process.maxMemory) {
+    return to_compare
+  }
+
+  try {
+    if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
+      return process.maxMemory
+    }
+    else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
+      return max_memory as nextflow.util.MemoryUnit
+    }
+    else {
+      return to_compare
+    }  
+  } catch (all) {
+        println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
+        System.exit(1)
+  }
+}
--- a/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
@@ -220,7 +220,7 @@ build_info:
  output: "target/executable/convert/from_spatialdata_to_h5mu"
  executable: "target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu"
  viash_version: "0.9.4"
-  git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+  git_commit: "798a0cb2692eaac648662732a05bb48f951f36a0"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu
+++ b/target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu
@@ -459,9 +459,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_spatialdata_to_h5mu"
-LABEL org.opencontainers.image.created="2025-08-22T08:22:47Z"
+LABEL org.opencontainers.image.created="2025-08-22T14:30:51Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+LABEL org.opencontainers.image.revision="798a0cb2692eaac648662732a05bb48f951f36a0"
 LABEL org.opencontainers.image.version="build_main"

 VIASHDOCKER
--- a/target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml
@@ -233,7 +233,7 @@ build_info:
  output: "target/executable/convert/from_xenium_to_h5mu"
  executable: "target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu"
  viash_version: "0.9.4"
-  git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+  git_commit: "798a0cb2692eaac648662732a05bb48f951f36a0"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu
+++ b/target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_xenium_to_h5mu"
-LABEL org.opencontainers.image.created="2025-08-22T08:22:47Z"
+LABEL org.opencontainers.image.created="2025-08-22T14:30:51Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+LABEL org.opencontainers.image.revision="798a0cb2692eaac648662732a05bb48f951f36a0"
 LABEL org.opencontainers.image.version="build_main"

 VIASHDOCKER
--- a/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml
+++ b/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml
@@ -314,7 +314,7 @@ build_info:
  output: "target/executable/convert/from_xenium_to_spatialdata"
  executable: "target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata"
  viash_version: "0.9.4"
-  git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+  git_commit: "798a0cb2692eaac648662732a05bb48f951f36a0"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata
+++ b/target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_xenium_to_spatialdata"
-LABEL org.opencontainers.image.created="2025-08-22T08:22:47Z"
+LABEL org.opencontainers.image.created="2025-08-22T14:30:51Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+LABEL org.opencontainers.image.revision="798a0cb2692eaac648662732a05bb48f951f36a0"
 LABEL org.opencontainers.image.version="build_main"

 VIASHDOCKER
--- a/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml
+++ b/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml
@@ -222,7 +222,7 @@ build_info:
  output: "target/executable/convert/from_xenium_to_spatialexperiment"
  executable: "target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment"
  viash_version: "0.9.4"
-  git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+  git_commit: "798a0cb2692eaac648662732a05bb48f951f36a0"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment
+++ b/target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment
@@ -457,9 +457,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("BiocManager", quietly

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_xenium_to_spatialexperiment"
-LABEL org.opencontainers.image.created="2025-08-22T08:22:47Z"
+LABEL org.opencontainers.image.created="2025-08-22T14:30:51Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+LABEL org.opencontainers.image.revision="798a0cb2692eaac648662732a05bb48f951f36a0"
 LABEL org.opencontainers.image.version="build_main"

 VIASHDOCKER
--- a/target/executable/filter/subset_cosmx/.config.vsh.yaml
+++ b/target/executable/filter/subset_cosmx/.config.vsh.yaml
@@ -227,7 +227,7 @@ build_info:
  output: "target/executable/filter/subset_cosmx"
  executable: "target/executable/filter/subset_cosmx/subset_cosmx"
  viash_version: "0.9.4"
-  git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+  git_commit: "798a0cb2692eaac648662732a05bb48f951f36a0"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/executable/filter/subset_cosmx/subset_cosmx
+++ b/target/executable/filter/subset_cosmx/subset_cosmx
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component filter subset_cosmx"
-LABEL org.opencontainers.image.created="2025-08-22T08:22:46Z"
+LABEL org.opencontainers.image.created="2025-08-22T14:30:50Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+LABEL org.opencontainers.image.revision="798a0cb2692eaac648662732a05bb48f951f36a0"
 LABEL org.opencontainers.image.version="build_main"

 VIASHDOCKER
--- a/target/executable/mapping/spaceranger_count/.config.vsh.yaml
+++ b/target/executable/mapping/spaceranger_count/.config.vsh.yaml
@@ -426,7 +426,7 @@ build_info:
  output: "target/executable/mapping/spaceranger_count"
  executable: "target/executable/mapping/spaceranger_count/spaceranger_count"
  viash_version: "0.9.4"
-  git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+  git_commit: "798a0cb2692eaac648662732a05bb48f951f36a0"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/executable/mapping/spaceranger_count/spaceranger_count
+++ b/target/executable/mapping/spaceranger_count/spaceranger_count
@@ -453,9 +453,9 @@ apt upgrade -y && apt install -y procps && rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.authors="Jakub Majercik"
 LABEL org.opencontainers.image.description="Companion container for running component mapping spaceranger_count"
-LABEL org.opencontainers.image.created="2025-08-22T08:22:48Z"
+LABEL org.opencontainers.image.created="2025-08-22T14:30:52Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+LABEL org.opencontainers.image.revision="798a0cb2692eaac648662732a05bb48f951f36a0"
 LABEL org.opencontainers.image.version="build_main"

 VIASHDOCKER
--- a/target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml
@@ -290,7 +290,7 @@ build_info:
  output: "target/nextflow/convert/from_cells2stats_to_h5mu"
  executable: "target/nextflow/convert/from_cells2stats_to_h5mu/main.nf"
  viash_version: "0.9.4"
-  git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+  git_commit: "798a0cb2692eaac648662732a05bb48f951f36a0"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/convert/from_cells2stats_to_h5mu/main.nf
+++ b/target/nextflow/convert/from_cells2stats_to_h5mu/main.nf
@@ -3382,7 +3382,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_cells2stats_to_h5mu",
    "viash_version" : "0.9.4",
-    "git_commit" : "6f308e6a3cca52f1283fbba734a3cdc858e18e1b",
+    "git_commit" : "798a0cb2692eaac648662732a05bb48f951f36a0",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml
@@ -225,7 +225,7 @@ build_info:
  output: "target/nextflow/convert/from_cosmx_to_h5mu"
  executable: "target/nextflow/convert/from_cosmx_to_h5mu/main.nf"
  viash_version: "0.9.4"
-  git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+  git_commit: "798a0cb2692eaac648662732a05bb48f951f36a0"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/convert/from_cosmx_to_h5mu/main.nf
+++ b/target/nextflow/convert/from_cosmx_to_h5mu/main.nf
@@ -3331,7 +3331,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_h5mu",
    "viash_version" : "0.9.4",
-    "git_commit" : "6f308e6a3cca52f1283fbba734a3cdc858e18e1b",
+    "git_commit" : "798a0cb2692eaac648662732a05bb48f951f36a0",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml
+++ b/target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml
@@ -232,7 +232,7 @@ build_info:
  output: "target/nextflow/convert/from_cosmx_to_spatialexperiment"
  executable: "target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf"
  viash_version: "0.9.4"
-  git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+  git_commit: "798a0cb2692eaac648662732a05bb48f951f36a0"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf
+++ b/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf
@@ -3322,7 +3322,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_spatialexperiment",
    "viash_version" : "0.9.4",
-    "git_commit" : "6f308e6a3cca52f1283fbba734a3cdc858e18e1b",
+    "git_commit" : "798a0cb2692eaac648662732a05bb48f951f36a0",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml
+++ b/target/nextflow/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml
@@ -0,0 +1,255 @@
+name: "from_h5mu_to_spatialexperiment"
+namespace: "convert"
+version: "build_main"
+authors:
+- name: "Dorien Roosen"
+  roles:
+  - "author"
+  info:
+    role: "Core Team Member"
+    links:
+      email: "dorien@data-intuitive.com"
+      github: "dorien-er"
+      linkedin: "dorien-roosen"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
+argument_groups:
+- name: "Arguments"
+  arguments:
+  - type: "file"
+    name: "--input"
+    alternatives:
+    - "-i"
+    description: "Input h5mu file"
+    info: null
+    example:
+    - "input.h5mu"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--modality"
+    description: "Name of the modality to be converted."
+    info: null
+    default:
+    - "rna"
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--obsm_spatial_coordinates"
+    description: "Key in the .obsm field that contains the spatial coordinates. \n\
+      Will be mapped to spatialCoords in the SpatialExperiment object.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output"
+    alternatives:
+    - "-o"
+    description: "Output SpatialExperiment file"
+    info: null
+    example:
+    - "output.rds"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "r_script"
+  path: "script.R"
+  is_executable: true
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
+description: "Converts an h5mu file into a SpatialExperiment object.\n"
+test_resources:
+- type: "r_script"
+  path: "test.R"
+  is_executable: true
+- type: "file"
+  path: "aviti_teton_tiny.h5mu"
+- type: "file"
+  path: "Lung5_Rep2_tiny.h5mu"
+- type: "file"
+  path: "xenium_tiny.h5mu"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+repositories:
+- type: "github"
+  name: "openpipeline"
+  repo: "openpipelines-bio/openpipeline"
+  tag: "2.1.2"
+links:
+  repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
+  docker_registry: "ghcr.io"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    label:
+    - "lowmem"
+    - "singlecpu"
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "rocker/r2u:22.04"
+  target_registry: "images.viash-hub.com"
+  target_tag: "build_main"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "libhdf5-dev"
+    - "libgeos-dev"
+    interactive: false
+  - type: "r"
+    cran:
+    - "hdf5r"
+    - "SpatialExperiment"
+    github:
+    - "scverse/anndataR@36f3caad9a7f360165c1510bbe0c62657580415a"
+    bioc_force_install: false
+    warnings_as_errors: true
+  test_setup:
+  - type: "docker"
+    env:
+    - "RETICULATE_PYTHON=/usr/bin/python"
+  - type: "apt"
+    packages:
+    - "python3"
+    - "python3-pip"
+    - "python3-dev"
+    - "python-is-python3"
+    interactive: false
+  - type: "r"
+    cran:
+    - "reticulate"
+    - "testthat"
+    bioc_force_install: false
+    warnings_as_errors: true
+  - type: "python"
+    user: false
+    packages:
+    - "anndata~=0.11.1"
+    - "mudata~=0.3.1"
+    script:
+    - "exec(\"try:\\n  import awkward\\nexcept ModuleNotFoundError:\\n  exit(0)\\\
+      nelse:  exit(1)\")"
+    upgrade: true
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/convert/from_h5mu_to_spatialexperiment/config.vsh.yaml"
+  runner: "nextflow"
+  engine: "docker|native"
+  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: "798a0cb2692eaac648662732a05bb48f951f36a0"
+  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
+package_config:
+  name: "openpipeline_spatial"
+  version: "build_main"
+  info:
+    test_resources:
+    - type: "s3"
+      path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
+      dest: "resources_test"
+  repositories:
+  - type: "github"
+    name: "openpipeline"
+    repo: "openpipelines-bio/openpipeline"
+    tag: "2.1.2"
+  viash_version: "0.9.4"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
+    .runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
+    )'"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'build_main'"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
+    docker_registry: "ghcr.io"
--- a/target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf
+++ b/target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf
--- a/target/nextflow/convert/from_h5mu_to_spatialexperiment/nextflow.config
+++ b/target/nextflow/convert/from_h5mu_to_spatialexperiment/nextflow.config
@@ -0,0 +1,126 @@
+manifest {
+  name = 'convert/from_h5mu_to_spatialexperiment'
+  mainScript = 'main.nf'
+  nextflowVersion = '!>=20.12.1-edge'
+  version = 'build_main'
+  description = 'Converts an h5mu file into a SpatialExperiment object.\n'
+  author = 'Dorien Roosen'
+}
+
+process.container = 'nextflow/bash:latest'
+
+// detect tempdir
+tempDir = java.nio.file.Paths.get(
+  System.getenv('NXF_TEMP') ?:
+    System.getenv('VIASH_TEMP') ?: 
+    System.getenv('TEMPDIR') ?: 
+    System.getenv('TMPDIR') ?: 
+    '/tmp'
+).toAbsolutePath()
+
+profiles {
+  no_publish {
+    process {
+      withName: '.*' {
+        publishDir = [
+          enabled: false
+        ]
+      }
+    }
+  }
+  mount_temp {
+    docker.temp            = tempDir
+    podman.temp            = tempDir
+    charliecloud.temp      = tempDir
+  }
+  docker {
+    docker.enabled         = true
+    // docker.userEmulation   = true
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  singularity {
+    singularity.enabled    = true
+    singularity.autoMounts = true
+    docker.enabled         = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  podman {
+    podman.enabled         = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  shifter {
+    shifter.enabled        = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    charliecloud.enabled   = false
+  }
+  charliecloud {
+    charliecloud.enabled   = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+  }
+}
+
+process{
+  withLabel: mem1gb { memory = 1000000000.B }
+  withLabel: mem2gb { memory = 2000000000.B }
+  withLabel: mem5gb { memory = 5000000000.B }
+  withLabel: mem10gb { memory = 10000000000.B }
+  withLabel: mem20gb { memory = 20000000000.B }
+  withLabel: mem50gb { memory = 50000000000.B }
+  withLabel: mem100gb { memory = 100000000000.B }
+  withLabel: mem200gb { memory = 200000000000.B }
+  withLabel: mem500gb { memory = 500000000000.B }
+  withLabel: mem1tb { memory = 1000000000000.B }
+  withLabel: mem2tb { memory = 2000000000000.B }
+  withLabel: mem5tb { memory = 5000000000000.B }
+  withLabel: mem10tb { memory = 10000000000000.B }
+  withLabel: mem20tb { memory = 20000000000000.B }
+  withLabel: mem50tb { memory = 50000000000000.B }
+  withLabel: mem100tb { memory = 100000000000000.B }
+  withLabel: mem200tb { memory = 200000000000000.B }
+  withLabel: mem500tb { memory = 500000000000000.B }
+  withLabel: mem1gib { memory = 1073741824.B }
+  withLabel: mem2gib { memory = 2147483648.B }
+  withLabel: mem4gib { memory = 4294967296.B }
+  withLabel: mem8gib { memory = 8589934592.B }
+  withLabel: mem16gib { memory = 17179869184.B }
+  withLabel: mem32gib { memory = 34359738368.B }
+  withLabel: mem64gib { memory = 68719476736.B }
+  withLabel: mem128gib { memory = 137438953472.B }
+  withLabel: mem256gib { memory = 274877906944.B }
+  withLabel: mem512gib { memory = 549755813888.B }
+  withLabel: mem1tib { memory = 1099511627776.B }
+  withLabel: mem2tib { memory = 2199023255552.B }
+  withLabel: mem4tib { memory = 4398046511104.B }
+  withLabel: mem8tib { memory = 8796093022208.B }
+  withLabel: mem16tib { memory = 17592186044416.B }
+  withLabel: mem32tib { memory = 35184372088832.B }
+  withLabel: mem64tib { memory = 70368744177664.B }
+  withLabel: mem128tib { memory = 140737488355328.B }
+  withLabel: mem256tib { memory = 281474976710656.B }
+  withLabel: mem512tib { memory = 562949953421312.B }
+  withLabel: cpu1 { cpus = 1 }
+  withLabel: cpu2 { cpus = 2 }
+  withLabel: cpu5 { cpus = 5 }
+  withLabel: cpu10 { cpus = 10 }
+  withLabel: cpu20 { cpus = 20 }
+  withLabel: cpu50 { cpus = 50 }
+  withLabel: cpu100 { cpus = 100 }
+  withLabel: cpu200 { cpus = 200 }
+  withLabel: cpu500 { cpus = 500 }
+  withLabel: cpu1000 { cpus = 1000 }
+}
+
+includeConfig("nextflow_labels.config")
--- a/target/nextflow/convert/from_h5mu_to_spatialexperiment/nextflow_labels.config
+++ b/target/nextflow/convert/from_h5mu_to_spatialexperiment/nextflow_labels.config
@@ -0,0 +1,68 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // CPU resources
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 4 }
+  withLabel: midcpu { cpus = 10 }
+  withLabel: highcpu { cpus = 20 }
+  
+  // Memory resources
+  withLabel: lowmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
+
+  // Disk space
+  // Nextflow apparently can't handle empty directives, i.e.
+  // withLabel: lowdisk {}
+  // so for that reason we have to add a dummy directive
+  withLabel: lowdisk {
+    dummyDirective = "dummyValue"
+  }
+  withLabel: middisk {
+    dummyDirective = "dummyValue"
+  }
+  withLabel: highdisk {
+    dummyDirective = "dummyValue"
+  }
+  withLabel: veryhighdisk {
+    dummyDirective = "dummyValue"
+  }
+  // NOTE: The above labels intentionally do not have an effect by default.
+  // The user should set the disk space requirements by adding the following
+  // to the compute environment:
+  //
+  // withLabel: lowdisk { disk = { 20.GB * task.attempt } }
+  // withLabel: middisk { disk = { 100.GB * task.attempt } }
+  // withLabel: highdisk { disk = { 200.GB * task.attempt } }
+  // withLabel: veryhighdisk { disk = { 500.GB * task.attempt } }
+}
+
+def get_memory(to_compare) {
+  if (!process.containsKey("maxMemory") || !process.maxMemory) {
+    return to_compare
+  }
+
+  try {
+    if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
+      return process.maxMemory
+    }
+    else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
+      return max_memory as nextflow.util.MemoryUnit
+    }
+    else {
+      return to_compare
+    }  
+  } catch (all) {
+        println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
+        System.exit(1)
+  }
+}
--- a/target/nextflow/convert/from_h5mu_to_spatialexperiment/nextflow_schema.json
+++ b/target/nextflow/convert/from_h5mu_to_spatialexperiment/nextflow_schema.json
@@ -0,0 +1,60 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "title": "from_h5mu_to_spatialexperiment",
+  "description": "Converts an h5mu file into a SpatialExperiment object.\n",
+  "type": "object",
+  "$defs": {
+    "arguments": {
+      "title": "Arguments",
+      "type": "object",
+      "description": "No description",
+      "properties": {
+        "input": {
+          "type": "string",
+          "format": "path",
+          "exists": true,
+          "description": "Input h5mu file",
+          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.h5mu\"`. "
+        },
+        "modality": {
+          "type": "string",
+          "description": "Name of the modality to be converted.",
+          "help_text": "Type: `string`, multiple: `False`, required, default: `\"rna\"`. ",
+          "default": "rna"
+        },
+        "obsm_spatial_coordinates": {
+          "type": "string",
+          "description": "Key in the .obsm field that contains the spatial coordinates",
+          "help_text": "Type: `string`, multiple: `False`. "
+        },
+        "output": {
+          "type": "string",
+          "format": "path",
+          "description": "Output SpatialExperiment file",
+          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.rds\"`, direction: `output`, example: `\"output.rds\"`. ",
+          "default": "$id.$key.output.rds"
+        }
+      }
+    },
+    "nextflow input-output arguments": {
+      "title": "Nextflow input-output arguments",
+      "type": "object",
+      "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
+      "properties": {
+        "publish_dir": {
+          "type": "string",
+          "description": "Path to an output directory.",
+          "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
+        }
+      }
+    }
+  },
+  "allOf": [
+    {
+      "$ref": "#/$defs/arguments"
+    },
+    {
+      "$ref": "#/$defs/nextflow input-output arguments"
+    }
+  ]
+}
--- a/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
@@ -220,7 +220,7 @@ build_info:
  output: "target/nextflow/convert/from_spatialdata_to_h5mu"
  executable: "target/nextflow/convert/from_spatialdata_to_h5mu/main.nf"
  viash_version: "0.9.4"
-  git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+  git_commit: "798a0cb2692eaac648662732a05bb48f951f36a0"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf
+++ b/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf
@@ -3330,7 +3330,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_spatialdata_to_h5mu",
    "viash_version" : "0.9.4",
-    "git_commit" : "6f308e6a3cca52f1283fbba734a3cdc858e18e1b",
+    "git_commit" : "798a0cb2692eaac648662732a05bb48f951f36a0",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml
@@ -233,7 +233,7 @@ build_info:
  output: "target/nextflow/convert/from_xenium_to_h5mu"
  executable: "target/nextflow/convert/from_xenium_to_h5mu/main.nf"
  viash_version: "0.9.4"
-  git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+  git_commit: "798a0cb2692eaac648662732a05bb48f951f36a0"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/convert/from_xenium_to_h5mu/main.nf
+++ b/target/nextflow/convert/from_xenium_to_h5mu/main.nf
@@ -3331,7 +3331,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_h5mu",
    "viash_version" : "0.9.4",
-    "git_commit" : "6f308e6a3cca52f1283fbba734a3cdc858e18e1b",
+    "git_commit" : "798a0cb2692eaac648662732a05bb48f951f36a0",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml
+++ b/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml
@@ -314,7 +314,7 @@ build_info:
  output: "target/nextflow/convert/from_xenium_to_spatialdata"
  executable: "target/nextflow/convert/from_xenium_to_spatialdata/main.nf"
  viash_version: "0.9.4"
-  git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+  git_commit: "798a0cb2692eaac648662732a05bb48f951f36a0"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/convert/from_xenium_to_spatialdata/main.nf
+++ b/target/nextflow/convert/from_xenium_to_spatialdata/main.nf
@@ -3425,7 +3425,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialdata",
    "viash_version" : "0.9.4",
-    "git_commit" : "6f308e6a3cca52f1283fbba734a3cdc858e18e1b",
+    "git_commit" : "798a0cb2692eaac648662732a05bb48f951f36a0",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml
+++ b/target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml
@@ -222,7 +222,7 @@ build_info:
  output: "target/nextflow/convert/from_xenium_to_spatialexperiment"
  executable: "target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf"
  viash_version: "0.9.4"
-  git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+  git_commit: "798a0cb2692eaac648662732a05bb48f951f36a0"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf
+++ b/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf
@@ -3311,7 +3311,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialexperiment",
    "viash_version" : "0.9.4",
-    "git_commit" : "6f308e6a3cca52f1283fbba734a3cdc858e18e1b",
+    "git_commit" : "798a0cb2692eaac648662732a05bb48f951f36a0",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/filter/subset_cosmx/.config.vsh.yaml
+++ b/target/nextflow/filter/subset_cosmx/.config.vsh.yaml
@@ -227,7 +227,7 @@ build_info:
  output: "target/nextflow/filter/subset_cosmx"
  executable: "target/nextflow/filter/subset_cosmx/main.nf"
  viash_version: "0.9.4"
-  git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+  git_commit: "798a0cb2692eaac648662732a05bb48f951f36a0"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/filter/subset_cosmx/main.nf
+++ b/target/nextflow/filter/subset_cosmx/main.nf
@@ -3333,7 +3333,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/filter/subset_cosmx",
    "viash_version" : "0.9.4",
-    "git_commit" : "6f308e6a3cca52f1283fbba734a3cdc858e18e1b",
+    "git_commit" : "798a0cb2692eaac648662732a05bb48f951f36a0",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml
+++ b/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml
@@ -426,7 +426,7 @@ build_info:
  output: "target/nextflow/mapping/spaceranger_count"
  executable: "target/nextflow/mapping/spaceranger_count/main.nf"
  viash_version: "0.9.4"
-  git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+  git_commit: "798a0cb2692eaac648662732a05bb48f951f36a0"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/mapping/spaceranger_count/main.nf
+++ b/target/nextflow/mapping/spaceranger_count/main.nf
@@ -3548,7 +3548,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/mapping/spaceranger_count",
    "viash_version" : "0.9.4",
-    "git_commit" : "6f308e6a3cca52f1283fbba734a3cdc858e18e1b",
+    "git_commit" : "798a0cb2692eaac648662732a05bb48f951f36a0",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml
+++ b/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml
@@ -644,7 +644,7 @@ build_info:
  output: "target/nextflow/workflows/multiomics/spatial_process_samples"
  executable: "target/nextflow/workflows/multiomics/spatial_process_samples/main.nf"
  viash_version: "0.9.4"
-  git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+  git_commit: "798a0cb2692eaac648662732a05bb48f951f36a0"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
  dependencies:
  - "target/dependencies/github/openpipelines-bio/openpipeline/disable-scrublet_build/nextflow/workflows/multiomics/process_samples"
--- a/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf
+++ b/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf
@@ -3813,7 +3813,7 @@ meta = [
    "engine" : "native",
    "output" : "/workdir/root/repo/target/nextflow/workflows/multiomics/spatial_process_samples",
    "viash_version" : "0.9.4",
-    "git_commit" : "6f308e6a3cca52f1283fbba734a3cdc858e18e1b",
+    "git_commit" : "798a0cb2692eaac648662732a05bb48f951f36a0",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml
+++ b/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml
@@ -387,7 +387,7 @@ build_info:
  output: "target/nextflow/workflows/qc/spatial_qc"
  executable: "target/nextflow/workflows/qc/spatial_qc/main.nf"
  viash_version: "0.9.4"
-  git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b"
+  git_commit: "798a0cb2692eaac648662732a05bb48f951f36a0"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
  dependencies:
  - "target/dependencies/github/openpipelines-bio/openpipeline/2.1.2/nextflow/workflows/qc/qc"
--- a/target/nextflow/workflows/qc/spatial_qc/main.nf
+++ b/target/nextflow/workflows/qc/spatial_qc/main.nf
@@ -3505,7 +3505,7 @@ meta = [
    "engine" : "native",
    "output" : "/workdir/root/repo/target/nextflow/workflows/qc/spatial_qc",
    "viash_version" : "0.9.4",
-    "git_commit" : "6f308e6a3cca52f1283fbba734a3cdc858e18e1b",
+    "git_commit" : "798a0cb2692eaac648662732a05bb48f951f36a0",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {