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Build branch openpipeline_spatial/downgrade-squidpy with version downgrade-squidpy to openpipeline_spatial on branch downgrade-squidpy (6ac22db)

Browse Source 
Build pipeline: openpipelines-bio.openpipeline-spatial.downgrade-squidpy-ntjcd

Source commit: 6ac22db107

Source message: update fov index
This commit is contained in:
CI
2025-11-18 16:15:26 +00:00
parent 42ebb8ebd2
commit 3ba70b6e6c
47 changed files with 145 additions and 103 deletions
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2
src/base/requirements/anndata.yaml
View File

@@ -1,2 +1,2 @@
packages:
- anndata<0.11.0
- anndata~=0.11.1

2
src/base/requirements/squidpy.yaml
View File

@@ -1,3 +1,3 @@
__merge__: [/src/base/requirements/spatialdata.yaml, .]
packages:
- squidpy<1.5.0
- squidpy~=1.6.5

26
src/convert/from_cosmx_to_h5mu/script.py
View File

@@ -63,12 +63,26 @@ def main():
logger.info("Reading in CosMx data...")
input_files = retrieve_input_data(par["input"])
adata = sq.read.nanostring(
path=input_files["counts_file"].parent,
counts_file=input_files["counts_file"].name,
meta_file=input_files["meta_file"].name,
fov_file=input_files["fov_file"].name,
)
try:
adata = sq.read.nanostring(
path=input_files["counts_file"].parent,
counts_file=input_files["counts_file"].name,
meta_file=input_files["meta_file"].name,
fov_file=input_files["fov_file"].name,
)
except ValueError as e:
if "Index fov invalid" in str(e):
import pandas as pd
df = pd.read_csv(input_files["fov_file"])
df.rename(columns={"FOV": "fov"}, inplace=True)
df.to_csv(input_files["fov_file"], index=False)
adata = sq.read.nanostring(
path=input_files["counts_file"].parent,
counts_file=input_files["counts_file"].name,
meta_file=input_files["meta_file"].name,
fov_file=input_files["fov_file"].name,
)
logger.info("Writing output MuData object...")
mdata = mu.MuData({par["modality"]: adata})

4
target/_private/executable/filter/subset_cosmx/.config.vsh.yaml
View File

@@ -203,7 +203,7 @@ engines:
packages:
- "spatialdata~=0.5.0"
- "pyarrow~=18.0.0"
- "squidpy<1.5.0"
- "squidpy~=1.6.5"
upgrade: true
test_setup:
- type: "apt"
@@ -228,7 +228,7 @@ build_info:
output: "target/_private/executable/filter/subset_cosmx"
executable: "target/_private/executable/filter/subset_cosmx/subset_cosmx"
viash_version: "0.9.4"
git_commit: "803b041ef1eeef9d77af23fa4544fa36e4ef3763"
git_commit: "6ac22db1075448735626eea2860ab5f3cd022348"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

6
target/_private/executable/filter/subset_cosmx/subset_cosmx
View File

@@ -454,13 +454,13 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "spatialdata~=0.5.0" "pyarrow~=18.0.0" "squidpy<1.5.0"
pip install --upgrade --no-cache-dir "spatialdata~=0.5.0" "pyarrow~=18.0.0" "squidpy~=1.6.5"
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="2025-11-18T15:22:07Z"
LABEL org.opencontainers.image.created="2025-11-18T15:52:47Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="803b041ef1eeef9d77af23fa4544fa36e4ef3763"
LABEL org.opencontainers.image.revision="6ac22db1075448735626eea2860ab5f3cd022348"
LABEL org.opencontainers.image.version="downgrade-squidpy"
VIASHDOCKER

4
target/_private/nextflow/filter/subset_cosmx/.config.vsh.yaml
View File

@@ -203,7 +203,7 @@ engines:
packages:
- "spatialdata~=0.5.0"
- "pyarrow~=18.0.0"
- "squidpy<1.5.0"
- "squidpy~=1.6.5"
upgrade: true
test_setup:
- type: "apt"
@@ -228,7 +228,7 @@ build_info:
output: "target/_private/nextflow/filter/subset_cosmx"
executable: "target/_private/nextflow/filter/subset_cosmx/main.nf"
viash_version: "0.9.4"
git_commit: "803b041ef1eeef9d77af23fa4544fa36e4ef3763"
git_commit: "6ac22db1075448735626eea2860ab5f3cd022348"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/_private/nextflow/filter/subset_cosmx/main.nf
View File

@@ -3297,7 +3297,7 @@ meta = [
"packages" : [
"spatialdata~=0.5.0",
"pyarrow~=18.0.0",
"squidpy<1.5.0"
"squidpy~=1.6.5"
],
"upgrade" : true
}
@@ -3334,7 +3334,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/_private/nextflow/filter/subset_cosmx",
"viash_version" : "0.9.4",
"git_commit" : "803b041ef1eeef9d77af23fa4544fa36e4ef3763",
"git_commit" : "6ac22db1075448735626eea2860ab5f3cd022348",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

4
target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml
View File

@@ -271,7 +271,7 @@ engines:
- type: "python"
user: false
packages:
- "anndata<0.11.0"
- "anndata~=0.11.1"
- "mudata~=0.3.1"
- "pyarrow"
git:
@@ -301,7 +301,7 @@ 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: "803b041ef1eeef9d77af23fa4544fa36e4ef3763"
git_commit: "6ac22db1075448735626eea2860ab5f3cd022348"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

6
target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu
View File

@@ -453,15 +453,15 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "anndata<0.11.0" "mudata~=0.3.1" "pyarrow" && \
pip install --upgrade --no-cache-dir "anndata~=0.11.1" "mudata~=0.3.1" "pyarrow" && \
pip install --upgrade --no-cache-dir "git+https://codeberg.org/miurahr/zipfile-inflate64.git@v0.2" && \
python -c 'exec("try:\n import awkward\nexcept ModuleNotFoundError:\n exit(0)\nelse: exit(1)")'
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="2025-11-18T15:22:07Z"
LABEL org.opencontainers.image.created="2025-11-18T15:52:48Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="803b041ef1eeef9d77af23fa4544fa36e4ef3763"
LABEL org.opencontainers.image.revision="6ac22db1075448735626eea2860ab5f3cd022348"
LABEL org.opencontainers.image.version="downgrade-squidpy"
VIASHDOCKER

8
target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml
View File

@@ -199,11 +199,11 @@ engines:
- type: "python"
user: false
packages:
- "anndata<0.11.0"
- "anndata~=0.11.1"
- "mudata~=0.3.1"
- "spatialdata~=0.5.0"
- "pyarrow~=18.0.0"
- "squidpy<1.5.0"
- "squidpy~=1.6.5"
- "pyarrow"
git:
- "https://codeberg.org/miurahr/zipfile-inflate64.git@v0.2"
@@ -230,7 +230,7 @@ engines:
- type: "python"
user: false
packages:
- "anndata<0.11.0"
- "anndata~=0.11.1"
- "mudata~=0.3.1"
script:
- "exec(\"try:\\n import awkward\\nexcept ModuleNotFoundError:\\n exit(0)\\\
@@ -247,7 +247,7 @@ 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: "803b041ef1eeef9d77af23fa4544fa36e4ef3763"
git_commit: "6ac22db1075448735626eea2860ab5f3cd022348"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

32
target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu
View File

@@ -454,15 +454,15 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "anndata<0.11.0" "mudata~=0.3.1" "spatialdata~=0.5.0" "pyarrow~=18.0.0" "squidpy<1.5.0" "pyarrow" && \
pip install --upgrade --no-cache-dir "anndata~=0.11.1" "mudata~=0.3.1" "spatialdata~=0.5.0" "pyarrow~=18.0.0" "squidpy~=1.6.5" "pyarrow" && \
pip install --upgrade --no-cache-dir "git+https://codeberg.org/miurahr/zipfile-inflate64.git@v0.2" && \
python -c 'exec("try:\n import awkward\nexcept ModuleNotFoundError:\n exit(0)\nelse: exit(1)")'
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="2025-11-18T15:22:07Z"
LABEL org.opencontainers.image.created="2025-11-18T15:52:48Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="803b041ef1eeef9d77af23fa4544fa36e4ef3763"
LABEL org.opencontainers.image.revision="6ac22db1075448735626eea2860ab5f3cd022348"
LABEL org.opencontainers.image.version="downgrade-squidpy"
VIASHDOCKER
@@ -1199,12 +1199,26 @@ def main():
logger.info("Reading in CosMx data...")
input_files = retrieve_input_data(par["input"])
adata = sq.read.nanostring(
path=input_files["counts_file"].parent,
counts_file=input_files["counts_file"].name,
meta_file=input_files["meta_file"].name,
fov_file=input_files["fov_file"].name,
)
try:
adata = sq.read.nanostring(
path=input_files["counts_file"].parent,
counts_file=input_files["counts_file"].name,
meta_file=input_files["meta_file"].name,
fov_file=input_files["fov_file"].name,
)
except ValueError as e:
if "Index fov invalid" in str(e):
import pandas as pd
df = pd.read_csv(input_files["fov_file"])
df.rename(columns={"FOV": "fov"}, inplace=True)
df.to_csv(input_files["fov_file"], index=False)
adata = sq.read.nanostring(
path=input_files["counts_file"].parent,
counts_file=input_files["counts_file"].name,
meta_file=input_files["meta_file"].name,
fov_file=input_files["fov_file"].name,
)
logger.info("Writing output MuData object...")
mdata = mu.MuData({par["modality"]: adata})

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

@@ -234,7 +234,7 @@ 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: "803b041ef1eeef9d77af23fa4544fa36e4ef3763"
git_commit: "6ac22db1075448735626eea2860ab5f3cd022348"
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="2025-11-18T15:22:07Z"
LABEL org.opencontainers.image.created="2025-11-18T15:52:48Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="803b041ef1eeef9d77af23fa4544fa36e4ef3763"
LABEL org.opencontainers.image.revision="6ac22db1075448735626eea2860ab5f3cd022348"
LABEL org.opencontainers.image.version="downgrade-squidpy"
VIASHDOCKER

4
target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml
View File

@@ -207,7 +207,7 @@ engines:
- type: "python"
user: false
packages:
- "anndata<0.11.0"
- "anndata~=0.11.1"
- "mudata~=0.3.1"
script:
- "exec(\"try:\\n import awkward\\nexcept ModuleNotFoundError:\\n exit(0)\\\
@@ -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: "803b041ef1eeef9d77af23fa4544fa36e4ef3763"
git_commit: "6ac22db1075448735626eea2860ab5f3cd022348"
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="2025-11-18T15:22:08Z"
LABEL org.opencontainers.image.created="2025-11-18T15:52:49Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="803b041ef1eeef9d77af23fa4544fa36e4ef3763"
LABEL org.opencontainers.image.revision="6ac22db1075448735626eea2860ab5f3cd022348"
LABEL org.opencontainers.image.version="downgrade-squidpy"
VIASHDOCKER

4
target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
View File

@@ -190,7 +190,7 @@ engines:
- type: "python"
user: false
packages:
- "anndata<0.11.0"
- "anndata~=0.11.1"
- "mudata~=0.3.1"
- "spatialdata~=0.5.0"
- "pyarrow~=18.0.0"
@@ -221,7 +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: "0.9.4"
git_commit: "803b041ef1eeef9d77af23fa4544fa36e4ef3763"
git_commit: "6ac22db1075448735626eea2860ab5f3cd022348"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

6
target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu
View File

@@ -454,14 +454,14 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "anndata<0.11.0" "mudata~=0.3.1" "spatialdata~=0.5.0" "pyarrow~=18.0.0" && \
pip install --upgrade --no-cache-dir "anndata~=0.11.1" "mudata~=0.3.1" "spatialdata~=0.5.0" "pyarrow~=18.0.0" && \
python -c 'exec("try:\n import awkward\nexcept ModuleNotFoundError:\n exit(0)\nelse: exit(1)")'
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="2025-11-18T15:22:07Z"
LABEL org.opencontainers.image.created="2025-11-18T15:52:48Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="803b041ef1eeef9d77af23fa4544fa36e4ef3763"
LABEL org.opencontainers.image.revision="6ac22db1075448735626eea2860ab5f3cd022348"
LABEL org.opencontainers.image.version="downgrade-squidpy"
VIASHDOCKER

4
target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml
View File

@@ -213,7 +213,7 @@ engines:
- type: "python"
user: false
packages:
- "anndata<0.11.0"
- "anndata~=0.11.1"
- "mudata~=0.3.1"
- "scanpy~=1.10.4"
- "pyarrow"
@@ -244,7 +244,7 @@ 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: "803b041ef1eeef9d77af23fa4544fa36e4ef3763"
git_commit: "6ac22db1075448735626eea2860ab5f3cd022348"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

6
target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu
View File

@@ -453,15 +453,15 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "anndata<0.11.0" "mudata~=0.3.1" "scanpy~=1.10.4" "pyarrow" && \
pip install --upgrade --no-cache-dir "anndata~=0.11.1" "mudata~=0.3.1" "scanpy~=1.10.4" "pyarrow" && \
pip install --upgrade --no-cache-dir "git+https://codeberg.org/miurahr/zipfile-inflate64.git@v0.2" && \
python -c 'exec("try:\n import awkward\nexcept ModuleNotFoundError:\n exit(0)\nelse: exit(1)")'
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="2025-11-18T15:22:07Z"
LABEL org.opencontainers.image.created="2025-11-18T15:52:48Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="803b041ef1eeef9d77af23fa4544fa36e4ef3763"
LABEL org.opencontainers.image.revision="6ac22db1075448735626eea2860ab5f3cd022348"
LABEL org.opencontainers.image.version="downgrade-squidpy"
VIASHDOCKER

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

@@ -326,7 +326,7 @@ 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: "803b041ef1eeef9d77af23fa4544fa36e4ef3763"
git_commit: "6ac22db1075448735626eea2860ab5f3cd022348"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata
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_xenium_to_spatialdata"
LABEL org.opencontainers.image.created="2025-11-18T15:22:07Z"
LABEL org.opencontainers.image.created="2025-11-18T15:52:48Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="803b041ef1eeef9d77af23fa4544fa36e4ef3763"
LABEL org.opencontainers.image.revision="6ac22db1075448735626eea2860ab5f3cd022348"
LABEL org.opencontainers.image.version="downgrade-squidpy"
VIASHDOCKER

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

@@ -224,7 +224,7 @@ 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: "803b041ef1eeef9d77af23fa4544fa36e4ef3763"
git_commit: "6ac22db1075448735626eea2860ab5f3cd022348"
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="2025-11-18T15:22:08Z"
LABEL org.opencontainers.image.created="2025-11-18T15:52:49Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="803b041ef1eeef9d77af23fa4544fa36e4ef3763"
LABEL org.opencontainers.image.revision="6ac22db1075448735626eea2860ab5f3cd022348"
LABEL org.opencontainers.image.version="downgrade-squidpy"
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: "803b041ef1eeef9d77af23fa4544fa36e4ef3763"
git_commit: "6ac22db1075448735626eea2860ab5f3cd022348"
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="2025-11-18T15:22:08Z"
LABEL org.opencontainers.image.created="2025-11-18T15:52:49Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="803b041ef1eeef9d77af23fa4544fa36e4ef3763"
LABEL org.opencontainers.image.revision="6ac22db1075448735626eea2860ab5f3cd022348"
LABEL org.opencontainers.image.version="downgrade-squidpy"
VIASHDOCKER

4
target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml
View File

@@ -271,7 +271,7 @@ engines:
- type: "python"
user: false
packages:
- "anndata<0.11.0"
- "anndata~=0.11.1"
- "mudata~=0.3.1"
- "pyarrow"
git:
@@ -301,7 +301,7 @@ 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: "803b041ef1eeef9d77af23fa4544fa36e4ef3763"
git_commit: "6ac22db1075448735626eea2860ab5f3cd022348"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/nextflow/convert/from_cells2stats_to_h5mu/main.nf
View File

@@ -3357,7 +3357,7 @@ meta = [
"type" : "python",
"user" : false,
"packages" : [
"anndata<0.11.0",
"anndata~=0.11.1",
"mudata~=0.3.1",
"pyarrow"
],
@@ -3399,7 +3399,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_cells2stats_to_h5mu",
"viash_version" : "0.9.4",
"git_commit" : "803b041ef1eeef9d77af23fa4544fa36e4ef3763",
"git_commit" : "6ac22db1075448735626eea2860ab5f3cd022348",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

8
target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml
View File

@@ -199,11 +199,11 @@ engines:
- type: "python"
user: false
packages:
- "anndata<0.11.0"
- "anndata~=0.11.1"
- "mudata~=0.3.1"
- "spatialdata~=0.5.0"
- "pyarrow~=18.0.0"
- "squidpy<1.5.0"
- "squidpy~=1.6.5"
- "pyarrow"
git:
- "https://codeberg.org/miurahr/zipfile-inflate64.git@v0.2"
@@ -230,7 +230,7 @@ engines:
- type: "python"
user: false
packages:
- "anndata<0.11.0"
- "anndata~=0.11.1"
- "mudata~=0.3.1"
script:
- "exec(\"try:\\n import awkward\\nexcept ModuleNotFoundError:\\n exit(0)\\\
@@ -247,7 +247,7 @@ 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: "803b041ef1eeef9d77af23fa4544fa36e4ef3763"
git_commit: "6ac22db1075448735626eea2860ab5f3cd022348"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

34
target/nextflow/convert/from_cosmx_to_h5mu/main.nf
View File

@@ -3295,11 +3295,11 @@ meta = [
"type" : "python",
"user" : false,
"packages" : [
"anndata<0.11.0",
"anndata~=0.11.1",
"mudata~=0.3.1",
"spatialdata~=0.5.0",
"pyarrow~=18.0.0",
"squidpy<1.5.0",
"squidpy~=1.6.5",
"pyarrow"
],
"git" : [
@@ -3341,7 +3341,7 @@ meta = [
"type" : "python",
"user" : false,
"packages" : [
"anndata<0.11.0",
"anndata~=0.11.1",
"mudata~=0.3.1"
],
"script" : [
@@ -3362,7 +3362,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_h5mu",
"viash_version" : "0.9.4",
"git_commit" : "803b041ef1eeef9d77af23fa4544fa36e4ef3763",
"git_commit" : "6ac22db1075448735626eea2860ab5f3cd022348",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {
@@ -3501,12 +3501,26 @@ def main():
logger.info("Reading in CosMx data...")
input_files = retrieve_input_data(par["input"])
adata = sq.read.nanostring(
path=input_files["counts_file"].parent,
counts_file=input_files["counts_file"].name,
meta_file=input_files["meta_file"].name,
fov_file=input_files["fov_file"].name,
)
try:
adata = sq.read.nanostring(
path=input_files["counts_file"].parent,
counts_file=input_files["counts_file"].name,
meta_file=input_files["meta_file"].name,
fov_file=input_files["fov_file"].name,
)
except ValueError as e:
if "Index fov invalid" in str(e):
import pandas as pd
df = pd.read_csv(input_files["fov_file"])
df.rename(columns={"FOV": "fov"}, inplace=True)
df.to_csv(input_files["fov_file"], index=False)
adata = sq.read.nanostring(
path=input_files["counts_file"].parent,
counts_file=input_files["counts_file"].name,
meta_file=input_files["meta_file"].name,
fov_file=input_files["fov_file"].name,
)
logger.info("Writing output MuData object...")
mdata = mu.MuData({par["modality"]: adata})

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

@@ -234,7 +234,7 @@ 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: "803b041ef1eeef9d77af23fa4544fa36e4ef3763"
git_commit: "6ac22db1075448735626eea2860ab5f3cd022348"
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

@@ -3326,7 +3326,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_spatialexperiment",
"viash_version" : "0.9.4",
"git_commit" : "803b041ef1eeef9d77af23fa4544fa36e4ef3763",
"git_commit" : "6ac22db1075448735626eea2860ab5f3cd022348",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

4
target/nextflow/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml
View File

@@ -207,7 +207,7 @@ engines:
- type: "python"
user: false
packages:
- "anndata<0.11.0"
- "anndata~=0.11.1"
- "mudata~=0.3.1"
script:
- "exec(\"try:\\n import awkward\\nexcept ModuleNotFoundError:\\n exit(0)\\\
@@ -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: "803b041ef1eeef9d77af23fa4544fa36e4ef3763"
git_commit: "6ac22db1075448735626eea2860ab5f3cd022348"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf
View File

@@ -3311,7 +3311,7 @@ meta = [
"type" : "python",
"user" : false,
"packages" : [
"anndata<0.11.0",
"anndata~=0.11.1",
"mudata~=0.3.1"
],
"script" : [
@@ -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" : "803b041ef1eeef9d77af23fa4544fa36e4ef3763",
"git_commit" : "6ac22db1075448735626eea2860ab5f3cd022348",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

4
target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
View File

@@ -190,7 +190,7 @@ engines:
- type: "python"
user: false
packages:
- "anndata<0.11.0"
- "anndata~=0.11.1"
- "mudata~=0.3.1"
- "spatialdata~=0.5.0"
- "pyarrow~=18.0.0"
@@ -221,7 +221,7 @@ build_info:
output: "target/nextflow/convert/from_spatialdata_to_h5mu"
executable: "target/nextflow/convert/from_spatialdata_to_h5mu/main.nf"
viash_version: "0.9.4"
git_commit: "803b041ef1eeef9d77af23fa4544fa36e4ef3763"
git_commit: "6ac22db1075448735626eea2860ab5f3cd022348"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/nextflow/convert/from_spatialdata_to_h5mu/main.nf
View File

@@ -3288,7 +3288,7 @@ meta = [
"type" : "python",
"user" : false,
"packages" : [
"anndata<0.11.0",
"anndata~=0.11.1",
"mudata~=0.3.1",
"spatialdata~=0.5.0",
"pyarrow~=18.0.0"
@@ -3331,7 +3331,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_spatialdata_to_h5mu",
"viash_version" : "0.9.4",
"git_commit" : "803b041ef1eeef9d77af23fa4544fa36e4ef3763",
"git_commit" : "6ac22db1075448735626eea2860ab5f3cd022348",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

4
target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml
View File

@@ -213,7 +213,7 @@ engines:
- type: "python"
user: false
packages:
- "anndata<0.11.0"
- "anndata~=0.11.1"
- "mudata~=0.3.1"
- "scanpy~=1.10.4"
- "pyarrow"
@@ -244,7 +244,7 @@ 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: "803b041ef1eeef9d77af23fa4544fa36e4ef3763"
git_commit: "6ac22db1075448735626eea2860ab5f3cd022348"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/nextflow/convert/from_xenium_to_h5mu/main.nf
View File

@@ -3305,7 +3305,7 @@ meta = [
"type" : "python",
"user" : false,
"packages" : [
"anndata<0.11.0",
"anndata~=0.11.1",
"mudata~=0.3.1",
"scanpy~=1.10.4",
"pyarrow"
@@ -3348,7 +3348,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_h5mu",
"viash_version" : "0.9.4",
"git_commit" : "803b041ef1eeef9d77af23fa4544fa36e4ef3763",
"git_commit" : "6ac22db1075448735626eea2860ab5f3cd022348",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

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

@@ -326,7 +326,7 @@ 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: "803b041ef1eeef9d77af23fa4544fa36e4ef3763"
git_commit: "6ac22db1075448735626eea2860ab5f3cd022348"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

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

@@ -3443,7 +3443,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialdata",
"viash_version" : "0.9.4",
"git_commit" : "803b041ef1eeef9d77af23fa4544fa36e4ef3763",
"git_commit" : "6ac22db1075448735626eea2860ab5f3cd022348",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

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

@@ -224,7 +224,7 @@ 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: "803b041ef1eeef9d77af23fa4544fa36e4ef3763"
git_commit: "6ac22db1075448735626eea2860ab5f3cd022348"
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

@@ -3315,7 +3315,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialexperiment",
"viash_version" : "0.9.4",
"git_commit" : "803b041ef1eeef9d77af23fa4544fa36e4ef3763",
"git_commit" : "6ac22db1075448735626eea2860ab5f3cd022348",
"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: "803b041ef1eeef9d77af23fa4544fa36e4ef3763"
git_commit: "6ac22db1075448735626eea2860ab5f3cd022348"
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" : "803b041ef1eeef9d77af23fa4544fa36e4ef3763",
"git_commit" : "6ac22db1075448735626eea2860ab5f3cd022348",
"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: "803b041ef1eeef9d77af23fa4544fa36e4ef3763"
git_commit: "6ac22db1075448735626eea2860ab5f3cd022348"
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" : "803b041ef1eeef9d77af23fa4544fa36e4ef3763",
"git_commit" : "6ac22db1075448735626eea2860ab5f3cd022348",
"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: "803b041ef1eeef9d77af23fa4544fa36e4ef3763"
git_commit: "6ac22db1075448735626eea2860ab5f3cd022348"
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" : "803b041ef1eeef9d77af23fa4544fa36e4ef3763",
"git_commit" : "6ac22db1075448735626eea2860ab5f3cd022348",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {