vsh/openpipeline_spatial
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Build branch allow-compressed-output-bundles with version allow-compressed-output-bundles (2cc934c)

Browse Source 
Build pipeline: openpipelines-bio.openpipeline-spatial.allow-compressed-ou59m5k

Source commit: 2cc934cef9

Source message: wip
This commit is contained in:
CI
2025-08-27 13:46:49 +00:00
parent 321cb96cfa
commit 008f51517b
62 changed files with 387 additions and 198 deletions
Download Patch File Download Diff File Expand all files Collapse all files

23
src/convert/from_cells2stats_to_h5mu/script.py
View File

@@ -173,23 +173,23 @@ def retrieve_input_data(cells2stats_output_bundle):
# │ └── RawCellStats.parquet
# └── Panel.json
required_files = [
"Panel.json",
"Cytoprofiling/Instrument/RawCellStats.parquet"
]
required_files = ["Panel.json", "Cytoprofiling/Instrument/RawCellStats.parquet"]
if zipfile.is_zipfile(cells2stats_output_bundle):
cells2stats_output_bundle = extract_selected_files_from_zip(
cells2stats_output_bundle,
members=required_files
cells2stats_output_bundle, members=required_files
)
assert os.path.isdir(cells2stats_output_bundle), "Input is expected to be a (compressed) directory."
assert os.path.isdir(cells2stats_output_bundle), (
"Input is expected to be a (compressed) directory."
)
input_dir = Path(cells2stats_output_bundle)
input_data = dict(zip(
["target_panel", "count_matrix"],
[input_dir / file for file in required_files]
))
input_data = dict(
zip(
["target_panel", "count_matrix"],
[input_dir / file for file in required_files],
)
)
assert all([file.exists() for file in input_data.values()]), (
f"Not all required input files are found. Make sure that {par['input']} contains {input_data.values()}."
@@ -199,7 +199,6 @@ def retrieve_input_data(cells2stats_output_bundle):
def main():
logger.info("Reading input data...")
input_data = retrieve_input_data(par["input"])
with open(input_data["target_panel"], "r") as f:

15
src/convert/from_cells2stats_to_h5mu/test.py
View File

@@ -56,15 +56,18 @@ def test_compressed_input(run_component, tmp_path):
output = tmp_path / "aviti.h5mu"
zipped_input = tmp_path / "aviti.zip"
subprocess.run(
["zip", "-r", str(zipped_input), "."],
cwd=input,
check=True
)
subprocess.run(["zip", "-r", str(zipped_input), "."], cwd=input, check=True)
# run component
run_component(
["--input", zipped_input, "--output", str(output), "--output_compression", "gzip"]
[
"--input",
zipped_input,
"--output",
str(output),
"--output_compression",
"gzip",
]
)
assert output.is_file(), "output file was not created"

29
src/convert/from_cosmx_to_h5mu/script.py
View File

@@ -4,7 +4,6 @@ import squidpy as sq
import mudata as mu
import glob
import zipfile
import os
## VIASH START
par = {
@@ -38,19 +37,29 @@ def retrieve_input_data(cosmx_output_bundle):
# ├── *_fov_positions_file.csv
# └── *_metadata_file.csv
expected_file_patterns = ["exprMat_file.csv", "fov_positions_file.csv", "metadata_file.csv"]
expected_file_patterns = [
"exprMat_file.csv",
"fov_positions_file.csv",
"metadata_file.csv",
]
if zipfile.is_zipfile(cosmx_output_bundle):
cosmx_output_bundle = extract_selected_files_from_zip(
cosmx_output_bundle,
members=["*" + file for file in expected_file_patterns]
cosmx_output_bundle, members=["*" + file for file in expected_file_patterns]
)
assert os.path.isdir(cosmx_output_bundle), "Input is expected to be a (compressed) directory."
assert os.path.isdir(cosmx_output_bundle), (
"Input is expected to be a (compressed) directory."
)
input_data = dict(zip(
["counts_file", "fov_file", "meta_file"],
[find_cosmx_files(cosmx_output_bundle, glob_pattern) for glob_pattern in expected_file_patterns]
))
input_data = dict(
zip(
["counts_file", "fov_file", "meta_file"],
[
find_cosmx_files(cosmx_output_bundle, glob_pattern)
for glob_pattern in expected_file_patterns
],
)
)
return input_data
@@ -63,7 +72,7 @@ def main():
path=par["input"],
counts_file=input_data["counts_file"],
meta_file=input_data["meta_file"],
fov_file=input_data["fov_file"]
fov_file=input_data["fov_file"],
)
logger.info("Writing output MuData object...")

11
src/convert/from_cosmx_to_h5mu/test.py
View File

@@ -3,6 +3,7 @@ import sys
import mudata as mu
import subprocess
def test_simple_execution(run_component, tmp_path):
output = tmp_path / "cosmx_tiny.h5mu"
@@ -57,13 +58,9 @@ def test_compressed_input(run_component, tmp_path):
output = tmp_path / "cosmx_tiny.h5mu"
zipped_input = tmp_path / "xenium_tiny.zip"
input = meta["resources_dir"] + "/Lung5_Rep2_tiny"
subprocess.run(
["zip", "-r", str(zipped_input), "."],
cwd=input,
check=True
)
subprocess.run(["zip", "-r", str(zipped_input), "."], cwd=input, check=True)
run_component(
[
"--input",

19
src/convert/from_xenium_to_h5mu/script.py
View File

@@ -37,22 +37,25 @@ def _retrieve_input_data(xenium_output_bundle):
"cell_feature_matrix.h5",
"cells.parquet",
"experiment.xenium",
"metrics_summary.csv"
"metrics_summary.csv",
]
if zipfile.is_zipfile(xenium_output_bundle):
xenium_output_bundle = extract_selected_files_from_zip(
xenium_output_bundle,
members=required_files
xenium_output_bundle, members=required_files
)
assert os.path.isdir(xenium_output_bundle), f"Input is expected to be a (compressed) directory."
assert os.path.isdir(xenium_output_bundle), (
"Input is expected to be a (compressed) directory."
)
input_dir = Path(xenium_output_bundle)
input_data = dict(zip(
["count_matrix", "cells_metadata", "experiment", "metrics_summary"],
[input_dir / file for file in required_files]
))
input_data = dict(
zip(
["count_matrix", "cells_metadata", "experiment", "metrics_summary"],
[input_dir / file for file in required_files],
)
)
assert all([file.exists() for file in input_data.values()]), (
f"Not all required input files are found. Make sure that {par['input']} contains {input_data.values()}."

15
src/convert/from_xenium_to_h5mu/test.py
View File

@@ -67,15 +67,18 @@ def test_compressed_input(run_component, tmp_path):
output = tmp_path / "xenium.h5mu"
zipped_input = tmp_path / "xenium_tiny.zip"
subprocess.run(
["zip", "-r", str(zipped_input), "."],
cwd=input,
check=True
)
subprocess.run(["zip", "-r", str(zipped_input), "."], cwd=input, check=True)
# run component
run_component(
["--input", zipped_input, "--output", str(output), "--output_compression", "gzip"]
[
"--input",
zipped_input,
"--output",
str(output),
"--output_compression",
"gzip",
]
)
assert output.is_file(), "output file was not created"

5
src/convert/from_xenium_to_spatialdata/config.vsh.yaml
View File

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

5
src/convert/from_xenium_to_spatialdata/script.py
View File

@@ -1,5 +1,6 @@
import sys
from spatialdata_io import xenium
import zipfile
## VIASH START
par = {
@@ -22,10 +23,14 @@ meta = {"resources_dir": "src/utils"}
sys.path.append(meta["resources_dir"])
from setup_logger import setup_logger
from unzip_archived_folder import unzip_archived_folder
logger = setup_logger()
logger.info("Reading in Xenium data...")
if zipfile.is_zipfile(par["input"]):
par["input"] = unzip_archived_folder(par["input"])
sdata = xenium(
par["input"],
cells_boundaries=par["cells_boundaries"],

31
src/convert/from_xenium_to_spatialdata/test.py
View File

@@ -2,6 +2,7 @@ import pytest
import os
import sys
import spatialdata as sd
import subprocess
def test_simple_execution(run_component, tmp_path):
@@ -31,5 +32,35 @@ def test_simple_execution(run_component, tmp_path):
assert (output_sd_path / "zmetadata").is_file(), "zmetadata file was not created"
def test_compressed_input(run_component, tmp_path):
output_sd_path = tmp_path / "sd"
input = meta["resources_dir"] + "/xenium_tiny"
zipped_input = tmp_path / "xenium_tiny.zip"
subprocess.run(["zip", "-r", str(zipped_input), "."], cwd=input, check=True)
run_component(
[
"--input",
zipped_input,
"--output",
output_sd_path,
]
)
assert os.path.exists(output_sd_path), "Output zarr folder was not created"
sdata = sd.read_zarr(output_sd_path)
assert isinstance(sdata, sd.SpatialData), (
"the generated output is not a SpatialData object"
)
assert os.path.exists(output_sd_path / "images"), "images folder was not created"
assert os.path.exists(output_sd_path / "labels"), "labels folder was not created"
assert os.path.exists(output_sd_path / "points"), "images folder was not created"
assert os.path.exists(output_sd_path / "shapes"), "shapes folder was not created"
assert os.path.exists(output_sd_path / "tables"), "tables folder was not created"
assert (output_sd_path / "zmetadata").is_file(), "zmetadata file was not created"
if __name__ == "__main__":
sys.exit(pytest.main([__file__]))

7
src/utils/unzip_archived_folder.py
View File

@@ -5,9 +5,7 @@ from pathlib import Path
from typing import Union
def unzip_archived_folder(
archived_folder: Union[str, Path]
) -> Union[str, Path]:
def unzip_archived_folder(archived_folder: Union[str, Path]) -> Union[str, Path]:
"""
Extracts a ZIP archive to a temporary directory and returns the path to the extracted folder.
@@ -26,8 +24,7 @@ def unzip_archived_folder(
def extract_selected_files_from_zip(
zip_path: Union[str, Path],
members: list[Union[str, Path]]
zip_path: Union[str, Path], members: list[Union[str, Path]]
) -> Union[str, Path]:
"""
Extracts selected files (supports glob patterns) from a ZIP archive to a temporary directory.

2
target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml
View File

@@ -296,7 +296,7 @@ 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: "b1bfccbd0edea3f1692c489d0f174f7e494a7341"
git_commit: "2cc934cef9746e6befa3e91c82080bc071294628"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

27
target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu
View File

@@ -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="2025-08-27T10:55:44Z"
LABEL org.opencontainers.image.created="2025-08-27T13:23:38Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="b1bfccbd0edea3f1692c489d0f174f7e494a7341"
LABEL org.opencontainers.image.revision="2cc934cef9746e6befa3e91c82080bc071294628"
LABEL org.opencontainers.image.version="allow-compressed-output-bundles"
VIASHDOCKER
@@ -1433,23 +1433,23 @@ def retrieve_input_data(cells2stats_output_bundle):
# │ └── RawCellStats.parquet
# └── Panel.json
required_files = [
"Panel.json",
"Cytoprofiling/Instrument/RawCellStats.parquet"
]
required_files = ["Panel.json", "Cytoprofiling/Instrument/RawCellStats.parquet"]
if zipfile.is_zipfile(cells2stats_output_bundle):
cells2stats_output_bundle = extract_selected_files_from_zip(
cells2stats_output_bundle,
members=required_files
cells2stats_output_bundle, members=required_files
)
assert os.path.isdir(cells2stats_output_bundle), "Input is expected to be a (compressed) directory."
assert os.path.isdir(cells2stats_output_bundle), (
"Input is expected to be a (compressed) directory."
)
input_dir = Path(cells2stats_output_bundle)
input_data = dict(zip(
["target_panel", "count_matrix"],
[input_dir / file for file in required_files]
))
input_data = dict(
zip(
["target_panel", "count_matrix"],
[input_dir / file for file in required_files],
)
)
assert all([file.exists() for file in input_data.values()]), (
f"Not all required input files are found. Make sure that {par['input']} contains {input_data.values()}."
@@ -1459,7 +1459,6 @@ def retrieve_input_data(cells2stats_output_bundle):
def main():
logger.info("Reading input data...")
input_data = retrieve_input_data(par["input"])
with open(input_data["target_panel"], "r") as f:

7
target/executable/convert/from_cells2stats_to_h5mu/unzip_archived_folder.py
View File

@@ -5,9 +5,7 @@ from pathlib import Path
from typing import Union
def unzip_archived_folder(
archived_folder: Union[str, Path]
) -> Union[str, Path]:
def unzip_archived_folder(archived_folder: Union[str, Path]) -> Union[str, Path]:
"""
Extracts a ZIP archive to a temporary directory and returns the path to the extracted folder.
@@ -26,8 +24,7 @@ def unzip_archived_folder(
def extract_selected_files_from_zip(
zip_path: Union[str, Path],
members: list[Union[str, Path]]
zip_path: Union[str, Path], members: list[Union[str, Path]]
) -> Union[str, Path]:
"""
Extracts selected files (supports glob patterns) from a ZIP archive to a temporary directory.

2
target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml
View File

@@ -231,7 +231,7 @@ 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: "b1bfccbd0edea3f1692c489d0f174f7e494a7341"
git_commit: "2cc934cef9746e6befa3e91c82080bc071294628"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

33
target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu
View File

@@ -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="2025-08-27T10:55:45Z"
LABEL org.opencontainers.image.created="2025-08-27T13:23:38Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="b1bfccbd0edea3f1692c489d0f174f7e494a7341"
LABEL org.opencontainers.image.revision="2cc934cef9746e6befa3e91c82080bc071294628"
LABEL org.opencontainers.image.version="allow-compressed-output-bundles"
VIASHDOCKER
@@ -1115,7 +1115,6 @@ import squidpy as sq
import mudata as mu
import glob
import zipfile
import os
## VIASH START
# The following code has been auto-generated by Viash.
@@ -1173,19 +1172,29 @@ def retrieve_input_data(cosmx_output_bundle):
# ├── *_fov_positions_file.csv
# └── *_metadata_file.csv
expected_file_patterns = ["exprMat_file.csv", "fov_positions_file.csv", "metadata_file.csv"]
expected_file_patterns = [
"exprMat_file.csv",
"fov_positions_file.csv",
"metadata_file.csv",
]
if zipfile.is_zipfile(cosmx_output_bundle):
cosmx_output_bundle = extract_selected_files_from_zip(
cosmx_output_bundle,
members=["*" + file for file in expected_file_patterns]
cosmx_output_bundle, members=["*" + file for file in expected_file_patterns]
)
assert os.path.isdir(cosmx_output_bundle), "Input is expected to be a (compressed) directory."
assert os.path.isdir(cosmx_output_bundle), (
"Input is expected to be a (compressed) directory."
)
input_data = dict(zip(
["counts_file", "fov_file", "meta_file"],
[find_cosmx_files(cosmx_output_bundle, glob_pattern) for glob_pattern in expected_file_patterns]
))
input_data = dict(
zip(
["counts_file", "fov_file", "meta_file"],
[
find_cosmx_files(cosmx_output_bundle, glob_pattern)
for glob_pattern in expected_file_patterns
],
)
)
return input_data
@@ -1198,7 +1207,7 @@ def main():
path=par["input"],
counts_file=input_data["counts_file"],
meta_file=input_data["meta_file"],
fov_file=input_data["fov_file"]
fov_file=input_data["fov_file"],
)
logger.info("Writing output MuData object...")

7
target/executable/convert/from_cosmx_to_h5mu/unzip_archived_folder.py
View File

@@ -5,9 +5,7 @@ from pathlib import Path
from typing import Union
def unzip_archived_folder(
archived_folder: Union[str, Path]
) -> Union[str, Path]:
def unzip_archived_folder(archived_folder: Union[str, Path]) -> Union[str, Path]:
"""
Extracts a ZIP archive to a temporary directory and returns the path to the extracted folder.
@@ -26,8 +24,7 @@ def unzip_archived_folder(
def extract_selected_files_from_zip(
zip_path: Union[str, Path],
members: list[Union[str, Path]]
zip_path: Union[str, Path], members: list[Union[str, Path]]
) -> Union[str, Path]:
"""
Extracts selected files (supports glob patterns) from a ZIP archive to a temporary directory.

2
target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml
View File

@@ -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: "b1bfccbd0edea3f1692c489d0f174f7e494a7341"
git_commit: "2cc934cef9746e6befa3e91c82080bc071294628"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment
View File

@@ -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="2025-08-27T10:55:44Z"
LABEL org.opencontainers.image.created="2025-08-27T13:23:37Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="b1bfccbd0edea3f1692c489d0f174f7e494a7341"
LABEL org.opencontainers.image.revision="2cc934cef9746e6befa3e91c82080bc071294628"
LABEL org.opencontainers.image.version="allow-compressed-output-bundles"
VIASHDOCKER

2
target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml
View File

@@ -224,7 +224,7 @@ build_info:
output: "target/executable/convert/from_h5mu_to_spatialexperiment"
executable: "target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment"
viash_version: "0.9.4"
git_commit: "b1bfccbd0edea3f1692c489d0f174f7e494a7341"
git_commit: "2cc934cef9746e6befa3e91c82080bc071294628"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment
View File

@@ -458,9 +458,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
LABEL org.opencontainers.image.authors="Dorien Roosen"
LABEL org.opencontainers.image.description="Companion container for running component convert from_h5mu_to_spatialexperiment"
LABEL org.opencontainers.image.created="2025-08-27T10:55:44Z"
LABEL org.opencontainers.image.created="2025-08-27T13:23:38Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="b1bfccbd0edea3f1692c489d0f174f7e494a7341"
LABEL org.opencontainers.image.revision="2cc934cef9746e6befa3e91c82080bc071294628"
LABEL org.opencontainers.image.version="allow-compressed-output-bundles"
VIASHDOCKER

2
target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
View File

@@ -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: "b1bfccbd0edea3f1692c489d0f174f7e494a7341"
git_commit: "2cc934cef9746e6befa3e91c82080bc071294628"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu
View File

@@ -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="2025-08-27T10:55:44Z"
LABEL org.opencontainers.image.created="2025-08-27T13:23:38Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="b1bfccbd0edea3f1692c489d0f174f7e494a7341"
LABEL org.opencontainers.image.revision="2cc934cef9746e6befa3e91c82080bc071294628"
LABEL org.opencontainers.image.version="allow-compressed-output-bundles"
VIASHDOCKER

2
target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml
View File

@@ -239,7 +239,7 @@ 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: "b1bfccbd0edea3f1692c489d0f174f7e494a7341"
git_commit: "2cc934cef9746e6befa3e91c82080bc071294628"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

23
target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu
View File

@@ -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="2025-08-27T10:55:44Z"
LABEL org.opencontainers.image.created="2025-08-27T13:23:37Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="b1bfccbd0edea3f1692c489d0f174f7e494a7341"
LABEL org.opencontainers.image.revision="2cc934cef9746e6befa3e91c82080bc071294628"
LABEL org.opencontainers.image.version="allow-compressed-output-bundles"
VIASHDOCKER
@@ -1212,22 +1212,25 @@ def _retrieve_input_data(xenium_output_bundle):
"cell_feature_matrix.h5",
"cells.parquet",
"experiment.xenium",
"metrics_summary.csv"
"metrics_summary.csv",
]
if zipfile.is_zipfile(xenium_output_bundle):
xenium_output_bundle = extract_selected_files_from_zip(
xenium_output_bundle,
members=required_files
xenium_output_bundle, members=required_files
)
assert os.path.isdir(xenium_output_bundle), f"Input is expected to be a (compressed) directory."
assert os.path.isdir(xenium_output_bundle), (
"Input is expected to be a (compressed) directory."
)
input_dir = Path(xenium_output_bundle)
input_data = dict(zip(
["count_matrix", "cells_metadata", "experiment", "metrics_summary"],
[input_dir / file for file in required_files]
))
input_data = dict(
zip(
["count_matrix", "cells_metadata", "experiment", "metrics_summary"],
[input_dir / file for file in required_files],
)
)
assert all([file.exists() for file in input_data.values()]), (
f"Not all required input files are found. Make sure that {par['input']} contains {input_data.values()}."

7
target/executable/convert/from_xenium_to_h5mu/unzip_archived_folder.py
View File

@@ -5,9 +5,7 @@ from pathlib import Path
from typing import Union
def unzip_archived_folder(
archived_folder: Union[str, Path]
) -> Union[str, Path]:
def unzip_archived_folder(archived_folder: Union[str, Path]) -> Union[str, Path]:
"""
Extracts a ZIP archive to a temporary directory and returns the path to the extracted folder.
@@ -26,8 +24,7 @@ def unzip_archived_folder(
def extract_selected_files_from_zip(
zip_path: Union[str, Path],
members: list[Union[str, Path]]
zip_path: Union[str, Path], members: list[Union[str, Path]]
) -> Union[str, Path]:
"""
Extracts selected files (supports glob patterns) from a ZIP archive to a temporary directory.

8
target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml
View File

@@ -173,6 +173,8 @@ resources:
is_executable: true
- type: "file"
path: "setup_logger.py"
- type: "file"
path: "unzip_archived_folder.py"
- type: "file"
path: "nextflow_labels.config"
dest: "nextflow_labels.config"
@@ -303,6 +305,10 @@ engines:
github:
- "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
upgrade: true
- type: "apt"
packages:
- "zip"
interactive: false
entrypoint: []
cmd: null
- type: "native"
@@ -314,7 +320,7 @@ 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: "b1bfccbd0edea3f1692c489d0f174f7e494a7341"
git_commit: "2cc934cef9746e6befa3e91c82080bc071294628"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

9
target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata
View File

@@ -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="2025-08-27T10:55:44Z"
LABEL org.opencontainers.image.created="2025-08-27T13:23:38Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="b1bfccbd0edea3f1692c489d0f174f7e494a7341"
LABEL org.opencontainers.image.revision="2cc934cef9746e6befa3e91c82080bc071294628"
LABEL org.opencontainers.image.version="allow-compressed-output-bundles"
VIASHDOCKER
@@ -1340,6 +1340,7 @@ trap interrupt INT SIGINT
cat > "\$tempscript" << 'VIASHMAIN'
import sys
from spatialdata_io import xenium
import zipfile
## VIASH START
# The following code has been auto-generated by Viash.
@@ -1386,10 +1387,14 @@ dep = {
sys.path.append(meta["resources_dir"])
from setup_logger import setup_logger
from unzip_archived_folder import unzip_archived_folder
logger = setup_logger()
logger.info("Reading in Xenium data...")
if zipfile.is_zipfile(par["input"]):
par["input"] = unzip_archived_folder(par["input"])
sdata = xenium(
par["input"],
cells_boundaries=par["cells_boundaries"],

50
target/executable/convert/from_xenium_to_spatialdata/unzip_archived_folder.py Normal file
View File

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

2
target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml
View File

@@ -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: "b1bfccbd0edea3f1692c489d0f174f7e494a7341"
git_commit: "2cc934cef9746e6befa3e91c82080bc071294628"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment
View File

@@ -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="2025-08-27T10:55:43Z"
LABEL org.opencontainers.image.created="2025-08-27T13:23:37Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="b1bfccbd0edea3f1692c489d0f174f7e494a7341"
LABEL org.opencontainers.image.revision="2cc934cef9746e6befa3e91c82080bc071294628"
LABEL org.opencontainers.image.version="allow-compressed-output-bundles"
VIASHDOCKER

2
target/executable/filter/subset_cosmx/.config.vsh.yaml
View File

@@ -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: "b1bfccbd0edea3f1692c489d0f174f7e494a7341"
git_commit: "2cc934cef9746e6befa3e91c82080bc071294628"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/executable/filter/subset_cosmx/subset_cosmx
View File

@@ -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="2025-08-27T10:55:43Z"
LABEL org.opencontainers.image.created="2025-08-27T13:23:37Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="b1bfccbd0edea3f1692c489d0f174f7e494a7341"
LABEL org.opencontainers.image.revision="2cc934cef9746e6befa3e91c82080bc071294628"
LABEL org.opencontainers.image.version="allow-compressed-output-bundles"
VIASHDOCKER

2
target/executable/mapping/spaceranger_count/.config.vsh.yaml
View File

@@ -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: "b1bfccbd0edea3f1692c489d0f174f7e494a7341"
git_commit: "2cc934cef9746e6befa3e91c82080bc071294628"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/executable/mapping/spaceranger_count/spaceranger_count
View File

@@ -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="2025-08-27T10:55:43Z"
LABEL org.opencontainers.image.created="2025-08-27T13:23:37Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="b1bfccbd0edea3f1692c489d0f174f7e494a7341"
LABEL org.opencontainers.image.revision="2cc934cef9746e6befa3e91c82080bc071294628"
LABEL org.opencontainers.image.version="allow-compressed-output-bundles"
VIASHDOCKER

2
target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml
View File

@@ -296,7 +296,7 @@ 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: "b1bfccbd0edea3f1692c489d0f174f7e494a7341"
git_commit: "2cc934cef9746e6befa3e91c82080bc071294628"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

25
target/nextflow/convert/from_cells2stats_to_h5mu/main.nf
View File

@@ -3393,7 +3393,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_cells2stats_to_h5mu",
"viash_version" : "0.9.4",
"git_commit" : "b1bfccbd0edea3f1692c489d0f174f7e494a7341",
"git_commit" : "2cc934cef9746e6befa3e91c82080bc071294628",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {
@@ -3642,23 +3642,23 @@ def retrieve_input_data(cells2stats_output_bundle):
# │ └── RawCellStats.parquet
# └── Panel.json
required_files = [
"Panel.json",
"Cytoprofiling/Instrument/RawCellStats.parquet"
]
required_files = ["Panel.json", "Cytoprofiling/Instrument/RawCellStats.parquet"]
if zipfile.is_zipfile(cells2stats_output_bundle):
cells2stats_output_bundle = extract_selected_files_from_zip(
cells2stats_output_bundle,
members=required_files
cells2stats_output_bundle, members=required_files
)
assert os.path.isdir(cells2stats_output_bundle), "Input is expected to be a (compressed) directory."
assert os.path.isdir(cells2stats_output_bundle), (
"Input is expected to be a (compressed) directory."
)
input_dir = Path(cells2stats_output_bundle)
input_data = dict(zip(
["target_panel", "count_matrix"],
[input_dir / file for file in required_files]
))
input_data = dict(
zip(
["target_panel", "count_matrix"],
[input_dir / file for file in required_files],
)
)
assert all([file.exists() for file in input_data.values()]), (
f"Not all required input files are found. Make sure that {par['input']} contains {input_data.values()}."
@@ -3668,7 +3668,6 @@ def retrieve_input_data(cells2stats_output_bundle):
def main():
logger.info("Reading input data...")
input_data = retrieve_input_data(par["input"])
with open(input_data["target_panel"], "r") as f:

7
target/nextflow/convert/from_cells2stats_to_h5mu/unzip_archived_folder.py
View File

@@ -5,9 +5,7 @@ from pathlib import Path
from typing import Union
def unzip_archived_folder(
archived_folder: Union[str, Path]
) -> Union[str, Path]:
def unzip_archived_folder(archived_folder: Union[str, Path]) -> Union[str, Path]:
"""
Extracts a ZIP archive to a temporary directory and returns the path to the extracted folder.
@@ -26,8 +24,7 @@ def unzip_archived_folder(
def extract_selected_files_from_zip(
zip_path: Union[str, Path],
members: list[Union[str, Path]]
zip_path: Union[str, Path], members: list[Union[str, Path]]
) -> Union[str, Path]:
"""
Extracts selected files (supports glob patterns) from a ZIP archive to a temporary directory.

2
target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml
View File

@@ -231,7 +231,7 @@ 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: "b1bfccbd0edea3f1692c489d0f174f7e494a7341"
git_commit: "2cc934cef9746e6befa3e91c82080bc071294628"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

31
target/nextflow/convert/from_cosmx_to_h5mu/main.nf
View File

@@ -3342,7 +3342,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_h5mu",
"viash_version" : "0.9.4",
"git_commit" : "b1bfccbd0edea3f1692c489d0f174f7e494a7341",
"git_commit" : "2cc934cef9746e6befa3e91c82080bc071294628",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {
@@ -3398,7 +3398,6 @@ import squidpy as sq
import mudata as mu
import glob
import zipfile
import os
## VIASH START
# The following code has been auto-generated by Viash.
@@ -3456,19 +3455,29 @@ def retrieve_input_data(cosmx_output_bundle):
# ├── *_fov_positions_file.csv
# └── *_metadata_file.csv
expected_file_patterns = ["exprMat_file.csv", "fov_positions_file.csv", "metadata_file.csv"]
expected_file_patterns = [
"exprMat_file.csv",
"fov_positions_file.csv",
"metadata_file.csv",
]
if zipfile.is_zipfile(cosmx_output_bundle):
cosmx_output_bundle = extract_selected_files_from_zip(
cosmx_output_bundle,
members=["*" + file for file in expected_file_patterns]
cosmx_output_bundle, members=["*" + file for file in expected_file_patterns]
)
assert os.path.isdir(cosmx_output_bundle), "Input is expected to be a (compressed) directory."
assert os.path.isdir(cosmx_output_bundle), (
"Input is expected to be a (compressed) directory."
)
input_data = dict(zip(
["counts_file", "fov_file", "meta_file"],
[find_cosmx_files(cosmx_output_bundle, glob_pattern) for glob_pattern in expected_file_patterns]
))
input_data = dict(
zip(
["counts_file", "fov_file", "meta_file"],
[
find_cosmx_files(cosmx_output_bundle, glob_pattern)
for glob_pattern in expected_file_patterns
],
)
)
return input_data
@@ -3481,7 +3490,7 @@ def main():
path=par["input"],
counts_file=input_data["counts_file"],
meta_file=input_data["meta_file"],
fov_file=input_data["fov_file"]
fov_file=input_data["fov_file"],
)
logger.info("Writing output MuData object...")

7
target/nextflow/convert/from_cosmx_to_h5mu/unzip_archived_folder.py
View File

@@ -5,9 +5,7 @@ from pathlib import Path
from typing import Union
def unzip_archived_folder(
archived_folder: Union[str, Path]
) -> Union[str, Path]:
def unzip_archived_folder(archived_folder: Union[str, Path]) -> Union[str, Path]:
"""
Extracts a ZIP archive to a temporary directory and returns the path to the extracted folder.
@@ -26,8 +24,7 @@ def unzip_archived_folder(
def extract_selected_files_from_zip(
zip_path: Union[str, Path],
members: list[Union[str, Path]]
zip_path: Union[str, Path], members: list[Union[str, Path]]
) -> Union[str, Path]:
"""
Extracts selected files (supports glob patterns) from a ZIP archive to a temporary directory.

2
target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml
View File

@@ -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: "b1bfccbd0edea3f1692c489d0f174f7e494a7341"
git_commit: "2cc934cef9746e6befa3e91c82080bc071294628"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

2
target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf
View File

@@ -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" : "b1bfccbd0edea3f1692c489d0f174f7e494a7341",
"git_commit" : "2cc934cef9746e6befa3e91c82080bc071294628",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

2
target/nextflow/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml
View File

@@ -224,7 +224,7 @@ build_info:
output: "target/nextflow/convert/from_h5mu_to_spatialexperiment"
executable: "target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf"
viash_version: "0.9.4"
git_commit: "b1bfccbd0edea3f1692c489d0f174f7e494a7341"
git_commit: "2cc934cef9746e6befa3e91c82080bc071294628"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

2
target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf
View File

@@ -3332,7 +3332,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_h5mu_to_spatialexperiment",
"viash_version" : "0.9.4",
"git_commit" : "b1bfccbd0edea3f1692c489d0f174f7e494a7341",
"git_commit" : "2cc934cef9746e6befa3e91c82080bc071294628",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

2
target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
View File

@@ -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: "b1bfccbd0edea3f1692c489d0f174f7e494a7341"
git_commit: "2cc934cef9746e6befa3e91c82080bc071294628"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

2
target/nextflow/convert/from_spatialdata_to_h5mu/main.nf
View File

@@ -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" : "b1bfccbd0edea3f1692c489d0f174f7e494a7341",
"git_commit" : "2cc934cef9746e6befa3e91c82080bc071294628",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

2
target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml
View File

@@ -239,7 +239,7 @@ 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: "b1bfccbd0edea3f1692c489d0f174f7e494a7341"
git_commit: "2cc934cef9746e6befa3e91c82080bc071294628"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

21
target/nextflow/convert/from_xenium_to_h5mu/main.nf
View File

@@ -3342,7 +3342,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_h5mu",
"viash_version" : "0.9.4",
"git_commit" : "b1bfccbd0edea3f1692c489d0f174f7e494a7341",
"git_commit" : "2cc934cef9746e6befa3e91c82080bc071294628",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {
@@ -3455,22 +3455,25 @@ def _retrieve_input_data(xenium_output_bundle):
"cell_feature_matrix.h5",
"cells.parquet",
"experiment.xenium",
"metrics_summary.csv"
"metrics_summary.csv",
]
if zipfile.is_zipfile(xenium_output_bundle):
xenium_output_bundle = extract_selected_files_from_zip(
xenium_output_bundle,
members=required_files
xenium_output_bundle, members=required_files
)
assert os.path.isdir(xenium_output_bundle), f"Input is expected to be a (compressed) directory."
assert os.path.isdir(xenium_output_bundle), (
"Input is expected to be a (compressed) directory."
)
input_dir = Path(xenium_output_bundle)
input_data = dict(zip(
["count_matrix", "cells_metadata", "experiment", "metrics_summary"],
[input_dir / file for file in required_files]
))
input_data = dict(
zip(
["count_matrix", "cells_metadata", "experiment", "metrics_summary"],
[input_dir / file for file in required_files],
)
)
assert all([file.exists() for file in input_data.values()]), (
f"Not all required input files are found. Make sure that {par['input']} contains {input_data.values()}."

7
target/nextflow/convert/from_xenium_to_h5mu/unzip_archived_folder.py
View File

@@ -5,9 +5,7 @@ from pathlib import Path
from typing import Union
def unzip_archived_folder(
archived_folder: Union[str, Path]
) -> Union[str, Path]:
def unzip_archived_folder(archived_folder: Union[str, Path]) -> Union[str, Path]:
"""
Extracts a ZIP archive to a temporary directory and returns the path to the extracted folder.
@@ -26,8 +24,7 @@ def unzip_archived_folder(
def extract_selected_files_from_zip(
zip_path: Union[str, Path],
members: list[Union[str, Path]]
zip_path: Union[str, Path], members: list[Union[str, Path]]
) -> Union[str, Path]:
"""
Extracts selected files (supports glob patterns) from a ZIP archive to a temporary directory.

8
target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml
View File

@@ -173,6 +173,8 @@ resources:
is_executable: true
- type: "file"
path: "setup_logger.py"
- type: "file"
path: "unzip_archived_folder.py"
- type: "file"
path: "nextflow_labels.config"
dest: "nextflow_labels.config"
@@ -303,6 +305,10 @@ engines:
github:
- "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
upgrade: true
- type: "apt"
packages:
- "zip"
interactive: false
entrypoint: []
cmd: null
- type: "native"
@@ -314,7 +320,7 @@ 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: "b1bfccbd0edea3f1692c489d0f174f7e494a7341"
git_commit: "2cc934cef9746e6befa3e91c82080bc071294628"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

18
target/nextflow/convert/from_xenium_to_spatialdata/main.nf
View File

@@ -3251,6 +3251,10 @@ meta = [
"type" : "file",
"path" : "/src/utils/setup_logger.py"
},
{
"type" : "file",
"path" : "/src/utils/unzip_archived_folder.py"
},
{
"type" : "file",
"path" : "/src/workflows/utils/labels.config",
@@ -3411,6 +3415,13 @@ meta = [
"openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
],
"upgrade" : true
},
{
"type" : "apt",
"packages" : [
"zip"
],
"interactive" : false
}
]
},
@@ -3425,7 +3436,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialdata",
"viash_version" : "0.9.4",
"git_commit" : "b1bfccbd0edea3f1692c489d0f174f7e494a7341",
"git_commit" : "2cc934cef9746e6befa3e91c82080bc071294628",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {
@@ -3477,6 +3488,7 @@ tempscript=".viash_script.py"
cat > "$tempscript" << VIASHMAIN
import sys
from spatialdata_io import xenium
import zipfile
## VIASH START
# The following code has been auto-generated by Viash.
@@ -3523,10 +3535,14 @@ dep = {
sys.path.append(meta["resources_dir"])
from setup_logger import setup_logger
from unzip_archived_folder import unzip_archived_folder
logger = setup_logger()
logger.info("Reading in Xenium data...")
if zipfile.is_zipfile(par["input"]):
par["input"] = unzip_archived_folder(par["input"])
sdata = xenium(
par["input"],
cells_boundaries=par["cells_boundaries"],

50
target/nextflow/convert/from_xenium_to_spatialdata/unzip_archived_folder.py Normal file
View File

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

2
target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml
View File

@@ -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: "b1bfccbd0edea3f1692c489d0f174f7e494a7341"
git_commit: "2cc934cef9746e6befa3e91c82080bc071294628"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

2
target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf
View File

@@ -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" : "b1bfccbd0edea3f1692c489d0f174f7e494a7341",
"git_commit" : "2cc934cef9746e6befa3e91c82080bc071294628",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

2
target/nextflow/filter/subset_cosmx/.config.vsh.yaml
View File

@@ -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: "b1bfccbd0edea3f1692c489d0f174f7e494a7341"
git_commit: "2cc934cef9746e6befa3e91c82080bc071294628"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

2
target/nextflow/filter/subset_cosmx/main.nf
View File

@@ -3333,7 +3333,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/filter/subset_cosmx",
"viash_version" : "0.9.4",
"git_commit" : "b1bfccbd0edea3f1692c489d0f174f7e494a7341",
"git_commit" : "2cc934cef9746e6befa3e91c82080bc071294628",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

2
target/nextflow/mapping/spaceranger_count/.config.vsh.yaml
View File

@@ -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: "b1bfccbd0edea3f1692c489d0f174f7e494a7341"
git_commit: "2cc934cef9746e6befa3e91c82080bc071294628"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

2
target/nextflow/mapping/spaceranger_count/main.nf
View File

@@ -3548,7 +3548,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/mapping/spaceranger_count",
"viash_version" : "0.9.4",
"git_commit" : "b1bfccbd0edea3f1692c489d0f174f7e494a7341",
"git_commit" : "2cc934cef9746e6befa3e91c82080bc071294628",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

2
target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml
View File

@@ -640,7 +640,7 @@ build_info:
output: "target/nextflow/workflows/multiomics/spatial_process_samples"
executable: "target/nextflow/workflows/multiomics/spatial_process_samples/main.nf"
viash_version: "0.9.4"
git_commit: "b1bfccbd0edea3f1692c489d0f174f7e494a7341"
git_commit: "2cc934cef9746e6befa3e91c82080bc071294628"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
dependencies:
- "target/dependencies/vsh/vsh/openpipeline/v3.0.0/nextflow/workflows/multiomics/process_samples"

2
target/nextflow/workflows/multiomics/spatial_process_samples/main.nf
View File

@@ -3807,7 +3807,7 @@ meta = [
"engine" : "native",
"output" : "/workdir/root/repo/target/nextflow/workflows/multiomics/spatial_process_samples",
"viash_version" : "0.9.4",
"git_commit" : "b1bfccbd0edea3f1692c489d0f174f7e494a7341",
"git_commit" : "2cc934cef9746e6befa3e91c82080bc071294628",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

2
target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml
View File

@@ -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: "b1bfccbd0edea3f1692c489d0f174f7e494a7341"
git_commit: "2cc934cef9746e6befa3e91c82080bc071294628"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
dependencies:
- "target/dependencies/vsh/vsh/openpipeline/v3.0.0/nextflow/workflows/qc/qc"

2
target/nextflow/workflows/qc/spatial_qc/main.nf
View File

@@ -3505,7 +3505,7 @@ meta = [
"engine" : "native",
"output" : "/workdir/root/repo/target/nextflow/workflows/qc/spatial_qc",
"viash_version" : "0.9.4",
"git_commit" : "b1bfccbd0edea3f1692c489d0f174f7e494a7341",
"git_commit" : "2cc934cef9746e6befa3e91c82080bc071294628",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {