Build branch build/main with version build_main (6ae6ad1)

Build pipeline: openpipelines-bio.openpipeline-spatial.build-main-h86dl

Source commit: 6ae6ad1936

Source message: deploy: 00cafd63af52decfa15830ba20bc88f7a9384965

.pre-commit-config.yaml

@@ -0,0 +1,24 @@
+
+repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.12.1
+  hooks:
+    - id: ruff-check
+      args: [ --fix ]
+    - id: ruff-format
+- repo: local
+  hooks:
+  - id: run_styler
+    name: run_styler
+    language: r
+    description: style files with {styler}
+    entry: "Rscript -e 'styler::style_file(commandArgs(TRUE))'"
+    files: '(\.[rR]profile|\.[rR]|\.[rR]md|\.[rR]nw|\.[qQ]md)$'
+    additional_dependencies: 
+      - styler
+      - knitr
+- repo: https://github.com/lorenzwalthert/precommit
+  rev: v0.4.3.9012 
+  hooks:
+    - id: lintr

CHANGELOG.md

@@ -2,4 +2,10 @@
 
 ## NEW FUNCTIONALITY
 
-* `mapping/spaceranger_count`: Added a spaceranger count component (PR #2).
+* `filter/subset_cosmx`: Added a component to subset COSMX data (PR #3).
+
+* `convert/from_cosmx_to_h5mu`: Added converter component for COSMX data (PR #3).
+
+* `mapping/spaceranger_count`: Added a spaceranger count component (PR #2).
+
+* `convert/from_spatialdata_to_h5mu`, `convert/from_xenium_to_spatialdata`: Added converter components for xenium data (PR #1).

_viash.yaml

@@ -10,7 +10,11 @@ repositories:
   - name: openpipeline
     repo: openpipelines-bio/openpipeline
     type: github
-    tag: main_build
+    tag: 2.1.2
+  - name: openpipeline_incubator
+    repo: openpipelines-bio/openpipeline_incubator
+    type: github
+    tag: main
 info:
   test_resources:
     - type: s3

ruff.toml

@@ -0,0 +1,43 @@
+# Exclude a variety of commonly ignored directories.
+exclude = [
+    ".git",
+    ".pyenv",
+    ".pytest_cache",
+    ".ruff_cache",
+    ".venv",
+    ".vscode",
+    "__pypackages__",
+    "_build",
+    "build",
+    "dist",
+    "node_modules",
+    "site-packages",
+]
+
+builtins = ["meta"]
+
+
+
+
+[format]
+# Like Black, use double quotes for strings.
+quote-style = "double"
+
+# Like Black, indent with spaces, rather than tabs.
+indent-style = "space"
+
+# Like Black, respect magic trailing commas.
+skip-magic-trailing-comma = false
+
+# Like Black, automatically detect the appropriate line ending.
+line-ending = "auto"
+
+[lint.flake8-pytest-style]
+fixture-parentheses = false
+mark-parentheses = false
+
+[lint]
+ignore = [
+  # module level import not at top of file
+  "E402"
+]

src/convert/from_cosmx_to_h5mu/script.py

@@ -9,11 +9,9 @@ par = {
     "output": "./resources_test/cosmx/Lung5_Rep2_tiny.h5mu",
     "dataset_id": "Lung5_Rep2",
     "modality": "rna",
-    "output_compression": None
-}
-meta ={
-    "resources_dir": "src/utils"
+    "output_compression": None,
 }
+meta = {"resources_dir": "src/utils"}
 ## VIASH END
 
 sys.path.append(meta["resources_dir"])
@@ -26,15 +24,14 @@ fov_file = f"{par['dataset_id']}_fov_positions_file.csv"
 meta_file = f"{par['dataset_id']}_metadata_file.csv"
 
 for file in [counts_file, fov_file, meta_file]:
-    assert os.path.isfile(os.path.join(par["input"], file)), f"File does not exist: {file}"
+    assert os.path.isfile(os.path.join(par["input"], file)), (
+        f"File does not exist: {file}"
+    )
 
 logger.info("Reading in CosMx data...")
 adata = sq.read.nanostring(
-    path=par["input"],
-    counts_file=counts_file,
-    meta_file=meta_file,
-    fov_file=fov_file
-    )
+    path=par["input"], counts_file=counts_file, meta_file=meta_file, fov_file=fov_file
+)
 
 logger.info("Writing output MuData object...")
 mdata = mu.MuData({par["modality"]: adata})

src/convert/from_cosmx_to_h5mu/test.py

@@ -2,15 +2,20 @@ import pytest
 import sys
 import mudata as mu
 
+
 def test_simple_execution(run_component, tmp_path):
     output = tmp_path / "cosmx_tiny.h5mu"
 
     run_component(
         [
-            "--input", meta["resources_dir"] + "/Lung5_Rep2_tiny",
-            "--dataset_id", "Lung5_Rep2",
-            "--num_fovs", "2",
-            "--output", output,
+            "--input",
+            meta["resources_dir"] + "/Lung5_Rep2_tiny",
+            "--dataset_id",
+            "Lung5_Rep2",
+            "--num_fovs",
+            "2",
+            "--output",
+            output,
         ]
     )
     assert output.is_file(), "output file was not created"
@@ -21,25 +26,25 @@ def test_simple_execution(run_component, tmp_path):
     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',
+        "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"
-        ]
+        "cell_ID",
+    ]
 
     assert list(adata.uns.keys()) == ["spatial"]
     assert list(adata.obsm.keys()) == ["spatial", "spatial_fov"]

src/convert/from_spatialdata_to_h5mu/script.py

@@ -7,11 +7,9 @@ par = {
     "input": "./resources_test/xenium/xenium_tiny.zarr",
     "output": "./resources_test/xenium/xenium_tiny.h5mu",
     "modality": "rna",
-    "output_compression": None
-}
-meta ={
-    "resources_dir": "src/utils"
+    "output_compression": None,
 }
+meta = {"resources_dir": "src/utils"}
 ## VIASH END
 
 sys.path.append(meta["resources_dir"])

src/convert/from_spatialdata_to_h5mu/test.py

@@ -2,40 +2,43 @@ import pytest
 import sys
 import mudata as mu
 
+
 def test_simple_execution(run_component, tmp_path):
     output = tmp_path / "output.h5mu"
 
     run_component(
         [
-            "--input", meta["resources_dir"] + "/xenium_tiny.zarr",
-            "--output", output,
+            "--input",
+            meta["resources_dir"] + "/xenium_tiny.zarr",
+            "--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"]
 
     # TODO: update what is checked here when spatialdata from other experimental set-ups are tested (e.g. cosmx, visium)
     assert list(adata.obs.keys()) == [
-        'cell_id',
-        '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',
-        'region',
-        'z_level',
-        'cell_labels'
-        ]
+        "cell_id",
+        "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",
+        "region",
+        "z_level",
+        "cell_labels",
+    ]
 
     assert list(adata.uns.keys()) == ["spatialdata_attrs"]
     assert list(adata.obsm.keys()) == ["spatial"]

src/convert/from_xenium_to_spatialdata/script.py

@@ -15,11 +15,9 @@ par = {
     "morphology_focus": True,
     "aligned_images": True,
     "cells_table": True,
-    "n_jobs": 1
-}
-meta ={
-    "resources_dir": "src/utils"
+    "n_jobs": 1,
 }
+meta = {"resources_dir": "src/utils"}
 ## VIASH END
 
 sys.path.append(meta["resources_dir"])
@@ -36,12 +34,12 @@ sdata = xenium(
     cells_labels=par["cells_labels"],
     nucleus_labels=par["nucleus_labels"],
     transcripts=par["transcripts"],
-    morphology_mip=par["morphology_mip"], # only available in version < 2.0.0
+    morphology_mip=par["morphology_mip"],  # only available in version < 2.0.0
     morphology_focus=par["morphology_focus"],
     aligned_images=par["aligned_images"],
     cells_table=par["cells_table"],
-    n_jobs=par["n_jobs"]
-    )
+    n_jobs=par["n_jobs"],
+)
 
 
 logger.info("Writing out SpatialData object to Zarr...")

src/convert/from_xenium_to_spatialdata/test.py

@@ -9,15 +9,19 @@ def test_simple_execution(run_component, tmp_path):
 
     run_component(
         [
-            "--input", meta["resources_dir"] + "/xenium_tiny",
-            "--output", output_sd_path,
+            "--input",
+            meta["resources_dir"] + "/xenium_tiny",
+            "--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 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"

src/filter/subset_cosmx/script.py

@@ -10,11 +10,9 @@ par = {
     "input": "./resources_test/cosmx/Lung5_Rep2",
     "output": "./resources_test/cosmx/Lung5_Rep2_tiny/",
     "dataset_id": "Lung5_Rep2",
-    "num_fovs": 5
-}
-meta ={
-    "resources_dir": "src/utils"
+    "num_fovs": 5,
 }
+meta = {"resources_dir": "src/utils"}
 ## VIASH END
 
 
@@ -29,7 +27,9 @@ meta_file = f"{par['dataset_id']}_metadata_file.csv"
 tx_file = f"{par['dataset_id']}_tx_file.csv"
 
 for file in [counts_file, fov_file, meta_file]:
-    assert os.path.isfile(os.path.join(par["input"], file)), f"File does not exist: {file}"
+    assert os.path.isfile(os.path.join(par["input"], file)), (
+        f"File does not exist: {file}"
+    )
 
 kept_fovs = list(range(1, par["num_fovs"] + 1))
 

src/filter/subset_cosmx/test.py

@@ -9,10 +9,14 @@ def test_simple_execution(run_component, tmp_path):
     dataset_id = "Lung5_Rep2"
     run_component(
         [
-            "--input", meta["resources_dir"] + "/Lung5_Rep2_tiny",
-            "--dataset_id", dataset_id,
-            "--num_fovs", "2",
-            "--output", output_path,
+            "--input",
+            meta["resources_dir"] + "/Lung5_Rep2_tiny",
+            "--dataset_id",
+            dataset_id,
+            "--num_fovs",
+            "2",
+            "--output",
+            output_path,
         ]
     )
 
@@ -28,7 +32,9 @@ def test_simple_execution(run_component, tmp_path):
 
     for image in images:
         assert os.path.exists(output_path / image), f"{image} folder was not created"
-        assert len(os.listdir(output_path / image)) == 2, f"{image} folder should contain 2 files"
+        assert len(os.listdir(output_path / image)) == 2, (
+            f"{image} folder should contain 2 files"
+        )
 
     for matrix in matrices:
         assert os.path.exists(matrix), f"{matrix} file was not created"

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

@@ -116,7 +116,11 @@ repositories:
 - type: "github"
   name: "openpipeline"
   repo: "openpipelines-bio/openpipeline"
-  tag: "main_build"
+  tag: "2.1.2"
+- type: "github"
+  name: "openpipeline_incubator"
+  repo: "openpipelines-bio/openpipeline_incubator"
+  tag: "main"
 links:
   repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
   docker_registry: "ghcr.io"
@@ -231,7 +235,7 @@ build_info:
   output: "target/executable/convert/from_cosmx_to_h5mu"
   executable: "target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu"
   viash_version: "0.9.3"
-  git_commit: "491efceaaf171f50aaa1d28f690c1e974cffc456"
+  git_commit: "6ae6ad193664a12a39c23f20030ebf03d9e886c6"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
@@ -245,7 +249,11 @@ package_config:
   - type: "github"
     name: "openpipeline"
     repo: "openpipelines-bio/openpipeline"
-    tag: "main_build"
+    tag: "2.1.2"
+  - type: "github"
+    name: "openpipeline_incubator"
+    repo: "openpipelines-bio/openpipeline_incubator"
+    tag: "main"
   viash_version: "0.9.3"
   source: "src"
   target: "target"

target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu

@@ -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_cosmx_to_h5mu"
-LABEL org.opencontainers.image.created="2025-07-10T12:30:15Z"
+LABEL org.opencontainers.image.created="2025-07-10T14:35:39Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="491efceaaf171f50aaa1d28f690c1e974cffc456"
+LABEL org.opencontainers.image.revision="6ae6ad193664a12a39c23f20030ebf03d9e886c6"
 LABEL org.opencontainers.image.version="build_main"
 
 VIASHDOCKER
@@ -1182,15 +1182,14 @@ fov_file = f"{par['dataset_id']}_fov_positions_file.csv"
 meta_file = f"{par['dataset_id']}_metadata_file.csv"
 
 for file in [counts_file, fov_file, meta_file]:
-    assert os.path.isfile(os.path.join(par["input"], file)), f"File does not exist: {file}"
+    assert os.path.isfile(os.path.join(par["input"], file)), (
+        f"File does not exist: {file}"
+    )
 
 logger.info("Reading in CosMx data...")
 adata = sq.read.nanostring(
-    path=par["input"],
-    counts_file=counts_file,
-    meta_file=meta_file,
-    fov_file=fov_file
-    )
+    path=par["input"], counts_file=counts_file, meta_file=meta_file, fov_file=fov_file
+)
 
 logger.info("Writing output MuData object...")
 mdata = mu.MuData({par["modality"]: adata})

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

@@ -101,7 +101,11 @@ repositories:
 - type: "github"
   name: "openpipeline"
   repo: "openpipelines-bio/openpipeline"
-  tag: "main_build"
+  tag: "2.1.2"
+- type: "github"
+  name: "openpipeline_incubator"
+  repo: "openpipelines-bio/openpipeline_incubator"
+  tag: "main"
 links:
   repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
   docker_registry: "ghcr.io"
@@ -217,7 +221,7 @@ build_info:
   output: "target/executable/convert/from_spatialdata_to_h5mu"
   executable: "target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu"
   viash_version: "0.9.3"
-  git_commit: "491efceaaf171f50aaa1d28f690c1e974cffc456"
+  git_commit: "6ae6ad193664a12a39c23f20030ebf03d9e886c6"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
@@ -231,7 +235,11 @@ package_config:
   - type: "github"
     name: "openpipeline"
     repo: "openpipelines-bio/openpipeline"
-    tag: "main_build"
+    tag: "2.1.2"
+  - type: "github"
+    name: "openpipeline_incubator"
+    repo: "openpipelines-bio/openpipeline_incubator"
+    tag: "main"
   viash_version: "0.9.3"
   source: "src"
   target: "target"

target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu

@@ -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_spatialdata_to_h5mu"
-LABEL org.opencontainers.image.created="2025-07-10T12:30:14Z"
+LABEL org.opencontainers.image.created="2025-07-10T14:35:39Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="491efceaaf171f50aaa1d28f690c1e974cffc456"
+LABEL org.opencontainers.image.revision="6ae6ad193664a12a39c23f20030ebf03d9e886c6"
 LABEL org.opencontainers.image.version="build_main"
 
 VIASHDOCKER

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

@@ -199,7 +199,11 @@ repositories:
 - type: "github"
   name: "openpipeline"
   repo: "openpipelines-bio/openpipeline"
-  tag: "main_build"
+  tag: "2.1.2"
+- type: "github"
+  name: "openpipeline_incubator"
+  repo: "openpipelines-bio/openpipeline_incubator"
+  tag: "main"
 links:
   repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
   docker_registry: "ghcr.io"
@@ -314,7 +318,7 @@ build_info:
   output: "target/executable/convert/from_xenium_to_spatialdata"
   executable: "target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata"
   viash_version: "0.9.3"
-  git_commit: "491efceaaf171f50aaa1d28f690c1e974cffc456"
+  git_commit: "6ae6ad193664a12a39c23f20030ebf03d9e886c6"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
@@ -328,7 +332,11 @@ package_config:
   - type: "github"
     name: "openpipeline"
     repo: "openpipelines-bio/openpipeline"
-    tag: "main_build"
+    tag: "2.1.2"
+  - type: "github"
+    name: "openpipeline_incubator"
+    repo: "openpipelines-bio/openpipeline_incubator"
+    tag: "main"
   viash_version: "0.9.3"
   source: "src"
   target: "target"

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="2025-07-10T12:30:14Z"
+LABEL org.opencontainers.image.created="2025-07-10T14:35:38Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="491efceaaf171f50aaa1d28f690c1e974cffc456"
+LABEL org.opencontainers.image.revision="6ae6ad193664a12a39c23f20030ebf03d9e886c6"
 LABEL org.opencontainers.image.version="build_main"
 
 VIASHDOCKER
@@ -1398,12 +1398,12 @@ sdata = xenium(
     cells_labels=par["cells_labels"],
     nucleus_labels=par["nucleus_labels"],
     transcripts=par["transcripts"],
-    morphology_mip=par["morphology_mip"], # only available in version < 2.0.0
+    morphology_mip=par["morphology_mip"],  # only available in version < 2.0.0
     morphology_focus=par["morphology_focus"],
     aligned_images=par["aligned_images"],
     cells_table=par["cells_table"],
-    n_jobs=par["n_jobs"]
-    )
+    n_jobs=par["n_jobs"],
+)
 
 
 logger.info("Writing out SpatialData object to Zarr...")

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

@@ -103,7 +103,11 @@ repositories:
 - type: "github"
   name: "openpipeline"
   repo: "openpipelines-bio/openpipeline"
-  tag: "main_build"
+  tag: "2.1.2"
+- type: "github"
+  name: "openpipeline_incubator"
+  repo: "openpipelines-bio/openpipeline_incubator"
+  tag: "main"
 links:
   repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
   docker_registry: "ghcr.io"
@@ -217,7 +221,7 @@ build_info:
   output: "target/executable/filter/subset_cosmx"
   executable: "target/executable/filter/subset_cosmx/subset_cosmx"
   viash_version: "0.9.3"
-  git_commit: "491efceaaf171f50aaa1d28f690c1e974cffc456"
+  git_commit: "6ae6ad193664a12a39c23f20030ebf03d9e886c6"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
@@ -231,7 +235,11 @@ package_config:
   - type: "github"
     name: "openpipeline"
     repo: "openpipelines-bio/openpipeline"
-    tag: "main_build"
+    tag: "2.1.2"
+  - type: "github"
+    name: "openpipeline_incubator"
+    repo: "openpipelines-bio/openpipeline_incubator"
+    tag: "main"
   viash_version: "0.9.3"
   source: "src"
   target: "target"

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="2025-07-10T12:30:14Z"
+LABEL org.opencontainers.image.created="2025-07-10T14:35:38Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="491efceaaf171f50aaa1d28f690c1e974cffc456"
+LABEL org.opencontainers.image.revision="6ae6ad193664a12a39c23f20030ebf03d9e886c6"
 LABEL org.opencontainers.image.version="build_main"
 
 VIASHDOCKER
@@ -1165,7 +1165,9 @@ meta_file = f"{par['dataset_id']}_metadata_file.csv"
 tx_file = f"{par['dataset_id']}_tx_file.csv"
 
 for file in [counts_file, fov_file, meta_file]:
-    assert os.path.isfile(os.path.join(par["input"], file)), f"File does not exist: {file}"
+    assert os.path.isfile(os.path.join(par["input"], file)), (
+        f"File does not exist: {file}"
+    )
 
 kept_fovs = list(range(1, par["num_fovs"] + 1))
 

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

@@ -329,7 +329,11 @@ repositories:
 - type: "github"
   name: "openpipeline"
   repo: "openpipelines-bio/openpipeline"
-  tag: "main_build"
+  tag: "2.1.2"
+- type: "github"
+  name: "openpipeline_incubator"
+  repo: "openpipelines-bio/openpipeline_incubator"
+  tag: "main"
 keywords:
 - "spaceranger"
 links:
@@ -426,7 +430,7 @@ build_info:
   output: "target/executable/mapping/spaceranger_count"
   executable: "target/executable/mapping/spaceranger_count/spaceranger_count"
   viash_version: "0.9.3"
-  git_commit: "491efceaaf171f50aaa1d28f690c1e974cffc456"
+  git_commit: "6ae6ad193664a12a39c23f20030ebf03d9e886c6"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
@@ -440,7 +444,11 @@ package_config:
   - type: "github"
     name: "openpipeline"
     repo: "openpipelines-bio/openpipeline"
-    tag: "main_build"
+    tag: "2.1.2"
+  - type: "github"
+    name: "openpipeline_incubator"
+    repo: "openpipelines-bio/openpipeline_incubator"
+    tag: "main"
   viash_version: "0.9.3"
   source: "src"
   target: "target"

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="2025-07-10T12:30:14Z"
+LABEL org.opencontainers.image.created="2025-07-10T14:35:38Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="491efceaaf171f50aaa1d28f690c1e974cffc456"
+LABEL org.opencontainers.image.revision="6ae6ad193664a12a39c23f20030ebf03d9e886c6"
 LABEL org.opencontainers.image.version="build_main"
 
 VIASHDOCKER

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

@@ -116,7 +116,11 @@ repositories:
 - type: "github"
   name: "openpipeline"
   repo: "openpipelines-bio/openpipeline"
-  tag: "main_build"
+  tag: "2.1.2"
+- type: "github"
+  name: "openpipeline_incubator"
+  repo: "openpipelines-bio/openpipeline_incubator"
+  tag: "main"
 links:
   repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
   docker_registry: "ghcr.io"
@@ -231,7 +235,7 @@ build_info:
   output: "target/nextflow/convert/from_cosmx_to_h5mu"
   executable: "target/nextflow/convert/from_cosmx_to_h5mu/main.nf"
   viash_version: "0.9.3"
-  git_commit: "491efceaaf171f50aaa1d28f690c1e974cffc456"
+  git_commit: "6ae6ad193664a12a39c23f20030ebf03d9e886c6"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
@@ -245,7 +249,11 @@ package_config:
   - type: "github"
     name: "openpipeline"
     repo: "openpipelines-bio/openpipeline"
-    tag: "main_build"
+    tag: "2.1.2"
+  - type: "github"
+    name: "openpipeline_incubator"
+    repo: "openpipelines-bio/openpipeline_incubator"
+    tag: "main"
   viash_version: "0.9.3"
   source: "src"
   target: "target"

target/nextflow/convert/from_cosmx_to_h5mu/main.nf

@@ -3194,7 +3194,13 @@ meta = [
       "type" : "github",
       "name" : "openpipeline",
       "repo" : "openpipelines-bio/openpipeline",
-      "tag" : "main_build"
+      "tag" : "2.1.2"
+    },
+    {
+      "type" : "github",
+      "name" : "openpipeline_incubator",
+      "repo" : "openpipelines-bio/openpipeline_incubator",
+      "tag" : "main"
     }
   ],
   "links" : {
@@ -3340,7 +3346,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_h5mu",
     "viash_version" : "0.9.3",
-    "git_commit" : "491efceaaf171f50aaa1d28f690c1e974cffc456",
+    "git_commit" : "6ae6ad193664a12a39c23f20030ebf03d9e886c6",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
@@ -3360,7 +3366,13 @@ meta = [
         "type" : "github",
         "name" : "openpipeline",
         "repo" : "openpipelines-bio/openpipeline",
-        "tag" : "main_build"
+        "tag" : "2.1.2"
+      },
+      {
+        "type" : "github",
+        "name" : "openpipeline_incubator",
+        "repo" : "openpipelines-bio/openpipeline_incubator",
+        "tag" : "main"
       }
     ],
     "viash_version" : "0.9.3",
@@ -3440,15 +3452,14 @@ fov_file = f"{par['dataset_id']}_fov_positions_file.csv"
 meta_file = f"{par['dataset_id']}_metadata_file.csv"
 
 for file in [counts_file, fov_file, meta_file]:
-    assert os.path.isfile(os.path.join(par["input"], file)), f"File does not exist: {file}"
+    assert os.path.isfile(os.path.join(par["input"], file)), (
+        f"File does not exist: {file}"
+    )
 
 logger.info("Reading in CosMx data...")
 adata = sq.read.nanostring(
-    path=par["input"],
-    counts_file=counts_file,
-    meta_file=meta_file,
-    fov_file=fov_file
-    )
+    path=par["input"], counts_file=counts_file, meta_file=meta_file, fov_file=fov_file
+)
 
 logger.info("Writing output MuData object...")
 mdata = mu.MuData({par["modality"]: adata})

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

@@ -101,7 +101,11 @@ repositories:
 - type: "github"
   name: "openpipeline"
   repo: "openpipelines-bio/openpipeline"
-  tag: "main_build"
+  tag: "2.1.2"
+- type: "github"
+  name: "openpipeline_incubator"
+  repo: "openpipelines-bio/openpipeline_incubator"
+  tag: "main"
 links:
   repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
   docker_registry: "ghcr.io"
@@ -217,7 +221,7 @@ build_info:
   output: "target/nextflow/convert/from_spatialdata_to_h5mu"
   executable: "target/nextflow/convert/from_spatialdata_to_h5mu/main.nf"
   viash_version: "0.9.3"
-  git_commit: "491efceaaf171f50aaa1d28f690c1e974cffc456"
+  git_commit: "6ae6ad193664a12a39c23f20030ebf03d9e886c6"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
@@ -231,7 +235,11 @@ package_config:
   - type: "github"
     name: "openpipeline"
     repo: "openpipelines-bio/openpipeline"
-    tag: "main_build"
+    tag: "2.1.2"
+  - type: "github"
+    name: "openpipeline_incubator"
+    repo: "openpipelines-bio/openpipeline_incubator"
+    tag: "main"
   viash_version: "0.9.3"
   source: "src"
   target: "target"

target/nextflow/convert/from_spatialdata_to_h5mu/main.nf

@@ -3185,7 +3185,13 @@ meta = [
       "type" : "github",
       "name" : "openpipeline",
       "repo" : "openpipelines-bio/openpipeline",
-      "tag" : "main_build"
+      "tag" : "2.1.2"
+    },
+    {
+      "type" : "github",
+      "name" : "openpipeline_incubator",
+      "repo" : "openpipelines-bio/openpipeline_incubator",
+      "tag" : "main"
     }
   ],
   "links" : {
@@ -3332,7 +3338,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_spatialdata_to_h5mu",
     "viash_version" : "0.9.3",
-    "git_commit" : "491efceaaf171f50aaa1d28f690c1e974cffc456",
+    "git_commit" : "6ae6ad193664a12a39c23f20030ebf03d9e886c6",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
@@ -3352,7 +3358,13 @@ meta = [
         "type" : "github",
         "name" : "openpipeline",
         "repo" : "openpipelines-bio/openpipeline",
-        "tag" : "main_build"
+        "tag" : "2.1.2"
+      },
+      {
+        "type" : "github",
+        "name" : "openpipeline_incubator",
+        "repo" : "openpipelines-bio/openpipeline_incubator",
+        "tag" : "main"
       }
     ],
     "viash_version" : "0.9.3",

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

@@ -199,7 +199,11 @@ repositories:
 - type: "github"
   name: "openpipeline"
   repo: "openpipelines-bio/openpipeline"
-  tag: "main_build"
+  tag: "2.1.2"
+- type: "github"
+  name: "openpipeline_incubator"
+  repo: "openpipelines-bio/openpipeline_incubator"
+  tag: "main"
 links:
   repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
   docker_registry: "ghcr.io"
@@ -314,7 +318,7 @@ build_info:
   output: "target/nextflow/convert/from_xenium_to_spatialdata"
   executable: "target/nextflow/convert/from_xenium_to_spatialdata/main.nf"
   viash_version: "0.9.3"
-  git_commit: "491efceaaf171f50aaa1d28f690c1e974cffc456"
+  git_commit: "6ae6ad193664a12a39c23f20030ebf03d9e886c6"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
@@ -328,7 +332,11 @@ package_config:
   - type: "github"
     name: "openpipeline"
     repo: "openpipelines-bio/openpipeline"
-    tag: "main_build"
+    tag: "2.1.2"
+  - type: "github"
+    name: "openpipeline_incubator"
+    repo: "openpipelines-bio/openpipeline_incubator"
+    tag: "main"
   viash_version: "0.9.3"
   source: "src"
   target: "target"

target/nextflow/convert/from_xenium_to_spatialdata/main.nf

@@ -3284,7 +3284,13 @@ meta = [
       "type" : "github",
       "name" : "openpipeline",
       "repo" : "openpipelines-bio/openpipeline",
-      "tag" : "main_build"
+      "tag" : "2.1.2"
+    },
+    {
+      "type" : "github",
+      "name" : "openpipeline_incubator",
+      "repo" : "openpipelines-bio/openpipeline_incubator",
+      "tag" : "main"
     }
   ],
   "links" : {
@@ -3430,7 +3436,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialdata",
     "viash_version" : "0.9.3",
-    "git_commit" : "491efceaaf171f50aaa1d28f690c1e974cffc456",
+    "git_commit" : "6ae6ad193664a12a39c23f20030ebf03d9e886c6",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
@@ -3450,7 +3456,13 @@ meta = [
         "type" : "github",
         "name" : "openpipeline",
         "repo" : "openpipelines-bio/openpipeline",
-        "tag" : "main_build"
+        "tag" : "2.1.2"
+      },
+      {
+        "type" : "github",
+        "name" : "openpipeline_incubator",
+        "repo" : "openpipelines-bio/openpipeline_incubator",
+        "tag" : "main"
       }
     ],
     "viash_version" : "0.9.3",
@@ -3540,12 +3552,12 @@ sdata = xenium(
     cells_labels=par["cells_labels"],
     nucleus_labels=par["nucleus_labels"],
     transcripts=par["transcripts"],
-    morphology_mip=par["morphology_mip"], # only available in version < 2.0.0
+    morphology_mip=par["morphology_mip"],  # only available in version < 2.0.0
     morphology_focus=par["morphology_focus"],
     aligned_images=par["aligned_images"],
     cells_table=par["cells_table"],
-    n_jobs=par["n_jobs"]
-    )
+    n_jobs=par["n_jobs"],
+)
 
 
 logger.info("Writing out SpatialData object to Zarr...")

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

@@ -103,7 +103,11 @@ repositories:
 - type: "github"
   name: "openpipeline"
   repo: "openpipelines-bio/openpipeline"
-  tag: "main_build"
+  tag: "2.1.2"
+- type: "github"
+  name: "openpipeline_incubator"
+  repo: "openpipelines-bio/openpipeline_incubator"
+  tag: "main"
 links:
   repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
   docker_registry: "ghcr.io"
@@ -217,7 +221,7 @@ build_info:
   output: "target/nextflow/filter/subset_cosmx"
   executable: "target/nextflow/filter/subset_cosmx/main.nf"
   viash_version: "0.9.3"
-  git_commit: "491efceaaf171f50aaa1d28f690c1e974cffc456"
+  git_commit: "6ae6ad193664a12a39c23f20030ebf03d9e886c6"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
@@ -231,7 +235,11 @@ package_config:
   - type: "github"
     name: "openpipeline"
     repo: "openpipelines-bio/openpipeline"
-    tag: "main_build"
+    tag: "2.1.2"
+  - type: "github"
+    name: "openpipeline_incubator"
+    repo: "openpipelines-bio/openpipeline_incubator"
+    tag: "main"
   viash_version: "0.9.3"
   source: "src"
   target: "target"

target/nextflow/filter/subset_cosmx/main.nf

@@ -3177,7 +3177,13 @@ meta = [
       "type" : "github",
       "name" : "openpipeline",
       "repo" : "openpipelines-bio/openpipeline",
-      "tag" : "main_build"
+      "tag" : "2.1.2"
+    },
+    {
+      "type" : "github",
+      "name" : "openpipeline_incubator",
+      "repo" : "openpipelines-bio/openpipeline_incubator",
+      "tag" : "main"
     }
   ],
   "links" : {
@@ -3322,7 +3328,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/filter/subset_cosmx",
     "viash_version" : "0.9.3",
-    "git_commit" : "491efceaaf171f50aaa1d28f690c1e974cffc456",
+    "git_commit" : "6ae6ad193664a12a39c23f20030ebf03d9e886c6",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
@@ -3342,7 +3348,13 @@ meta = [
         "type" : "github",
         "name" : "openpipeline",
         "repo" : "openpipelines-bio/openpipeline",
-        "tag" : "main_build"
+        "tag" : "2.1.2"
+      },
+      {
+        "type" : "github",
+        "name" : "openpipeline_incubator",
+        "repo" : "openpipelines-bio/openpipeline_incubator",
+        "tag" : "main"
       }
     ],
     "viash_version" : "0.9.3",
@@ -3425,7 +3437,9 @@ meta_file = f"{par['dataset_id']}_metadata_file.csv"
 tx_file = f"{par['dataset_id']}_tx_file.csv"
 
 for file in [counts_file, fov_file, meta_file]:
-    assert os.path.isfile(os.path.join(par["input"], file)), f"File does not exist: {file}"
+    assert os.path.isfile(os.path.join(par["input"], file)), (
+        f"File does not exist: {file}"
+    )
 
 kept_fovs = list(range(1, par["num_fovs"] + 1))
 

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

@@ -329,7 +329,11 @@ repositories:
 - type: "github"
   name: "openpipeline"
   repo: "openpipelines-bio/openpipeline"
-  tag: "main_build"
+  tag: "2.1.2"
+- type: "github"
+  name: "openpipeline_incubator"
+  repo: "openpipelines-bio/openpipeline_incubator"
+  tag: "main"
 keywords:
 - "spaceranger"
 links:
@@ -426,7 +430,7 @@ build_info:
   output: "target/nextflow/mapping/spaceranger_count"
   executable: "target/nextflow/mapping/spaceranger_count/main.nf"
   viash_version: "0.9.3"
-  git_commit: "491efceaaf171f50aaa1d28f690c1e974cffc456"
+  git_commit: "6ae6ad193664a12a39c23f20030ebf03d9e886c6"
   git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
   name: "openpipeline_spatial"
@@ -440,7 +444,11 @@ package_config:
   - type: "github"
     name: "openpipeline"
     repo: "openpipelines-bio/openpipeline"
-    tag: "main_build"
+    tag: "2.1.2"
+  - type: "github"
+    name: "openpipeline_incubator"
+    repo: "openpipelines-bio/openpipeline_incubator"
+    tag: "main"
   viash_version: "0.9.3"
   source: "src"
   target: "target"

target/nextflow/mapping/spaceranger_count/main.nf

@@ -3437,7 +3437,13 @@ meta = [
       "type" : "github",
       "name" : "openpipeline",
       "repo" : "openpipelines-bio/openpipeline",
-      "tag" : "main_build"
+      "tag" : "2.1.2"
+    },
+    {
+      "type" : "github",
+      "name" : "openpipeline_incubator",
+      "repo" : "openpipelines-bio/openpipeline_incubator",
+      "tag" : "main"
     }
   ],
   "keywords" : [
@@ -3553,7 +3559,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/mapping/spaceranger_count",
     "viash_version" : "0.9.3",
-    "git_commit" : "491efceaaf171f50aaa1d28f690c1e974cffc456",
+    "git_commit" : "6ae6ad193664a12a39c23f20030ebf03d9e886c6",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
   },
   "package_config" : {
@@ -3573,7 +3579,13 @@ meta = [
         "type" : "github",
         "name" : "openpipeline",
         "repo" : "openpipelines-bio/openpipeline",
-        "tag" : "main_build"
+        "tag" : "2.1.2"
+      },
+      {
+        "type" : "github",
+        "name" : "openpipeline_incubator",
+        "repo" : "openpipelines-bio/openpipeline_incubator",
+        "tag" : "main"
       }
     ],
     "viash_version" : "0.9.3",