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Build branch build/main with version build_main (226d7de)

Browse Source 
Build pipeline: openpipelines-bio.openpipeline-spatial.build-main-vdjx9

Source commit: 226d7de695

Source message: deploy: 46b97b56724d241439f09d3748315a26f03a300d
This commit is contained in:
CI
2025-08-18 08:17:10 +00:00
parent 72b5c7c839
commit b1ffb24eb9
49 changed files with 165 additions and 127 deletions
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2
src/base/requirements/anndata.yaml Normal file
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@@ -0,0 +1,2 @@
packages:
- anndata~=0.11.1

5
src/base/requirements/anndata_mudata.yaml Normal file
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@@ -0,0 +1,5 @@
__merge__: [/src/base/requirements/anndata.yaml, .]
packages:
- mudata~=0.3.1
script: |
exec("try:\n import awkward\nexcept ModuleNotFoundError:\n exit(0)\nelse: exit(1)")

2
src/base/requirements/openpipeline_testutils.yaml Normal file
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@@ -0,0 +1,2 @@
github:
- openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils

8
src/base/requirements/python_test_setup.yaml Normal file
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@@ -0,0 +1,8 @@
test_setup:
- type: apt
packages:
- git
- type: python
__merge__:
- /src/base/requirements/viashpy.yaml
- /src/base/requirements/openpipeline_testutils.yaml

2
src/base/requirements/scanpy.yaml Normal file
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@@ -0,0 +1,2 @@
packages:
- scanpy~=1.10.4

3
src/base/requirements/spatialdata-io.yaml Normal file
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@@ -0,0 +1,3 @@
__merge__: [/src/base/requirements/spatialdata.yaml, .]
packages:
- spatialdata-io~=0.2.0

2
src/base/requirements/spatialdata.yaml Normal file
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@@ -0,0 +1,2 @@
packages:
- spatialdata~=0.4.1rc

3
src/base/requirements/squidpy.yaml Normal file
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@@ -0,0 +1,3 @@
__merge__: [/src/base/requirements/spatialdata.yaml, .]
packages:
- squidpy~=1.6.5

2
src/base/requirements/viashpy.yaml Normal file
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@@ -0,0 +1,2 @@
packages:
- viashpy==0.9.0

13
src/convert/from_cosmx_to_h5mu/config.vsh.yaml
View File

@@ -52,17 +52,8 @@ engines:
packages:
- procps
- type: python
packages:
- squidpy~=1.6.5
- mudata~=0.3.1
test_setup:
- type: apt
packages:
- git
- type: python
packages:
- viashpy==0.8.0
github: openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils
__merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/squidpy.yaml]
__merge__: [ /src/base/requirements/python_test_setup.yaml, .]
runners:
- type: executable
- type: nextflow

6
src/convert/from_cosmx_to_spatialexperiment/script.R
View File

@@ -6,12 +6,14 @@ par <- list(
add_tx_path = TRUE,
add_polygon_path = FALSE,
add_fov_positions = TRUE,
alternative_experiment_features = c("NegPrb", "Negative", "SystemControl", "FalseCode"),
alternative_experiment_features = c(
"NegPrb", "Negative", "SystemControl", "FalseCode"
),
output = "spe_cosmx_test.rds"
)
### VIASH END
if (par$add_polygon_path == FALSE & par$add_tx_path == FALSE) {
if (par$add_polygon_path == FALSE && par$add_tx_path == FALSE) {
add_parquet_paths <- FALSE
} else {
add_parquet_paths <- TRUE

12
src/convert/from_cosmx_to_spatialexperiment/test.R
View File

@@ -4,7 +4,7 @@ library(SpatialExperiment)
## VIASH START
meta <- list(
executable = "target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment",
executable = "./from_cosmx_to_spatialexperiment",
resources_dir = "resources_test/cosmx/",
name = "from_cosmx_to_spatialexperiment"
)
@@ -42,7 +42,10 @@ expect_is(obj, "SpatialExperiment")
# Assay structure
expect_equal(names(slot(obj, "assays")), "counts")
# Spatial coordinates
expect_equal(spatialCoordsNames(obj), c("CenterX_global_px", "CenterY_global_px"))
expect_equal(
spatialCoordsNames(obj),
c("CenterX_global_px", "CenterY_global_px")
)
# Alternative experiments
expect_equal(altExpNames(obj), c("NegPrb"))
# Metadata components
@@ -96,7 +99,10 @@ expect_is(obj_ext, "SpatialExperiment")
# Assay structure
expect_equal(names(slot(obj_ext, "assays")), "counts")
# Spatial coordinates
expect_equal(spatialCoordsNames(obj_ext), c("CenterX_global_px", "CenterY_global_px"))
expect_equal(
spatialCoordsNames(obj_ext),
c("CenterX_global_px", "CenterY_global_px")
)
# Alternative experiments
expect_length(altExpNames(obj_ext), 0)
# Metadata components

14
src/convert/from_spatialdata_to_h5mu/config.vsh.yaml
View File

@@ -46,18 +46,8 @@ engines:
packages:
- procps
- type: python
packages:
- spatialdata~=0.4.0
- spatialdata-io~=0.2.0
- mudata~=0.3.1
test_setup:
- type: apt
packages:
- git
- type: python
packages:
- viashpy==0.8.0
github: openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils
__merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/spatialdata.yaml]
__merge__: [ /src/base/requirements/python_test_setup.yaml, .]
runners:
- type: executable
- type: nextflow

13
src/convert/from_xenium_to_spatialdata/config.vsh.yaml
View File

@@ -90,17 +90,8 @@ engines:
packages:
- procps
- type: python
packages:
- spatialdata-io~=0.1.7
test_setup:
- type: apt
packages:
- git
- type: python
packages:
- viashpy==0.8.0
- spatialdata~=0.3.0
github: openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils
__merge__: [ /src/base/requirements/spatialdata-io.yaml ]
__merge__: [ /src/base/requirements/python_test_setup.yaml, .]
runners:
- type: executable
- type: nextflow

5
src/convert/from_xenium_to_spatialexperiment/script.R
View File

@@ -5,7 +5,10 @@ par <- list(
input = "resources_test/xenium/xenium_tiny",
add_experiment_xenium = TRUE,
add_parquet_paths = TRUE,
alternative_experiment_features = c("NegControlProbe", "UnassignedCodeword", "NegControlCodeword", "antisense", "BLANK"),
alternative_experiment_features = c(
"NegControlProbe", "UnassignedCodeword",
"NegControlCodeword", "antisense", "BLANK"
),
output = "spe_test.rds"
)
### VIASH END

11
src/convert/from_xenium_to_spatialexperiment/test.R
View File

@@ -4,7 +4,7 @@ library(SpatialExperiment)
## VIASH START
meta <- list(
executable = "target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment",
executable = "./from_xenium_to_spatialexperiment",
resources_dir = "resources_test/xenium",
name = "from_xenium_to_spatial_experiment"
)
@@ -42,9 +42,14 @@ expect_equal(names(slot(obj, "assays")), "counts")
# Spatial coordinates
expect_equal(spatialCoordsNames(obj), c("x_centroid", "y_centroid"))
# Alternative experiments
expect_equal(altExpNames(obj), c("NegControlProbe", "UnassignedCodeword", "NegControlCodeword"))
expect_equal(
altExpNames(obj),
c("NegControlProbe", "UnassignedCodeword", "NegControlCodeword")
)
# Metadata components
metadata_components <- c("experiment.xenium", "transcripts", "cell_boundaries", "nucleus_boundaries")
metadata_components <- c(
"experiment.xenium", "transcripts", "cell_boundaries", "nucleus_boundaries"
)
expect_named(
metadata(obj),
metadata_components,

12
src/filter/subset_cosmx/config.vsh.yaml
View File

@@ -62,16 +62,8 @@ engines:
packages:
- procps
- type: python
packages:
- squidpy~=1.6.5
test_setup:
- type: apt
packages:
- git
- type: python
packages:
- viashpy==0.8.0
github: openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils
__merge__: [ /src/base/requirements/squidpy.yaml ]
__merge__: [ /src/base/requirements/python_test_setup.yaml, .]
runners:
- type: executable
- type: nextflow

11
target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml
View File

@@ -198,8 +198,13 @@ engines:
- type: "python"
user: false
packages:
- "squidpy~=1.6.5"
- "anndata~=0.11.1"
- "mudata~=0.3.1"
- "spatialdata~=0.4.1rc"
- "squidpy~=1.6.5"
script:
- "exec(\"try:\\n import awkward\\nexcept ModuleNotFoundError:\\n exit(0)\\\
nelse: exit(1)\")"
upgrade: true
test_setup:
- type: "apt"
@@ -209,7 +214,7 @@ engines:
- type: "python"
user: false
packages:
- "viashpy==0.8.0"
- "viashpy==0.9.0"
github:
- "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
upgrade: true
@@ -224,7 +229,7 @@ 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: "280b21fc21238c6e7b2e76089deffdef5d979b34"
git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

7
target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu
View File

@@ -454,13 +454,14 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "squidpy~=1.6.5" "mudata~=0.3.1"
pip install --upgrade --no-cache-dir "anndata~=0.11.1" "mudata~=0.3.1" "spatialdata~=0.4.1rc" "squidpy~=1.6.5" && \
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="2025-07-24T15:22:52Z"
LABEL org.opencontainers.image.created="2025-08-18T07:54:17Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="280b21fc21238c6e7b2e76089deffdef5d979b34"
LABEL org.opencontainers.image.revision="226d7de695d56f116dd1ba8e08a51ebf63b153b3"
LABEL org.opencontainers.image.version="build_main"
VIASHDOCKER

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

@@ -236,7 +236,7 @@ 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: "280b21fc21238c6e7b2e76089deffdef5d979b34"
git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

6
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="2025-07-24T15:22:53Z"
LABEL org.opencontainers.image.created="2025-08-18T07:54:16Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="280b21fc21238c6e7b2e76089deffdef5d979b34"
LABEL org.opencontainers.image.revision="226d7de695d56f116dd1ba8e08a51ebf63b153b3"
LABEL org.opencontainers.image.version="build_main"
VIASHDOCKER
@@ -1221,7 +1221,7 @@ rm(.viash_orig_warn)
### VIASH END
if (par\$add_polygon_path == FALSE & par\$add_tx_path == FALSE) {
if (par\$add_polygon_path == FALSE && par\$add_tx_path == FALSE) {
add_parquet_paths <- FALSE
} else {
add_parquet_paths <- TRUE

11
target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
View File

@@ -194,9 +194,12 @@ engines:
- type: "python"
user: false
packages:
- "spatialdata~=0.4.0"
- "spatialdata-io~=0.2.0"
- "anndata~=0.11.1"
- "mudata~=0.3.1"
- "spatialdata~=0.4.1rc"
script:
- "exec(\"try:\\n import awkward\\nexcept ModuleNotFoundError:\\n exit(0)\\\
nelse: exit(1)\")"
upgrade: true
test_setup:
- type: "apt"
@@ -206,7 +209,7 @@ engines:
- type: "python"
user: false
packages:
- "viashpy==0.8.0"
- "viashpy==0.9.0"
github:
- "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
upgrade: true
@@ -221,7 +224,7 @@ 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: "280b21fc21238c6e7b2e76089deffdef5d979b34"
git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

7
target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu
View File

@@ -454,13 +454,14 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "spatialdata~=0.4.0" "spatialdata-io~=0.2.0" "mudata~=0.3.1"
pip install --upgrade --no-cache-dir "anndata~=0.11.1" "mudata~=0.3.1" "spatialdata~=0.4.1rc" && \
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="2025-07-24T15:22:52Z"
LABEL org.opencontainers.image.created="2025-08-18T07:54:16Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="280b21fc21238c6e7b2e76089deffdef5d979b34"
LABEL org.opencontainers.image.revision="226d7de695d56f116dd1ba8e08a51ebf63b153b3"
LABEL org.opencontainers.image.version="build_main"
VIASHDOCKER

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

@@ -292,7 +292,8 @@ engines:
- type: "python"
user: false
packages:
- "spatialdata-io~=0.1.7"
- "spatialdata~=0.4.1rc"
- "spatialdata-io~=0.2.0"
upgrade: true
test_setup:
- type: "apt"
@@ -302,8 +303,7 @@ engines:
- type: "python"
user: false
packages:
- "viashpy==0.8.0"
- "spatialdata~=0.3.0"
- "viashpy==0.9.0"
github:
- "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
upgrade: true
@@ -318,7 +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: "0.9.4"
git_commit: "280b21fc21238c6e7b2e76089deffdef5d979b34"
git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

6
target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata
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-io~=0.1.7"
pip install --upgrade --no-cache-dir "spatialdata~=0.4.1rc" "spatialdata-io~=0.2.0"
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="2025-07-24T15:22:52Z"
LABEL org.opencontainers.image.created="2025-08-18T07:54:17Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="280b21fc21238c6e7b2e76089deffdef5d979b34"
LABEL org.opencontainers.image.revision="226d7de695d56f116dd1ba8e08a51ebf63b153b3"
LABEL org.opencontainers.image.version="build_main"
VIASHDOCKER

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

@@ -226,7 +226,7 @@ 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: "280b21fc21238c6e7b2e76089deffdef5d979b34"
git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
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="2025-07-24T15:22:53Z"
LABEL org.opencontainers.image.created="2025-08-18T07:54:16Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="280b21fc21238c6e7b2e76089deffdef5d979b34"
LABEL org.opencontainers.image.revision="226d7de695d56f116dd1ba8e08a51ebf63b153b3"
LABEL org.opencontainers.image.version="build_main"
VIASHDOCKER

5
target/executable/filter/subset_cosmx/.config.vsh.yaml
View File

@@ -205,6 +205,7 @@ engines:
- type: "python"
user: false
packages:
- "spatialdata~=0.4.1rc"
- "squidpy~=1.6.5"
upgrade: true
test_setup:
@@ -215,7 +216,7 @@ engines:
- type: "python"
user: false
packages:
- "viashpy==0.8.0"
- "viashpy==0.9.0"
github:
- "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
upgrade: true
@@ -230,7 +231,7 @@ build_info:
output: "target/executable/filter/subset_cosmx"
executable: "target/executable/filter/subset_cosmx/subset_cosmx"
viash_version: "0.9.4"
git_commit: "280b21fc21238c6e7b2e76089deffdef5d979b34"
git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

6
target/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 "squidpy~=1.6.5"
pip install --upgrade --no-cache-dir "spatialdata~=0.4.1rc" "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="2025-07-24T15:22:52Z"
LABEL org.opencontainers.image.created="2025-08-18T07:54:16Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="280b21fc21238c6e7b2e76089deffdef5d979b34"
LABEL org.opencontainers.image.revision="226d7de695d56f116dd1ba8e08a51ebf63b153b3"
LABEL org.opencontainers.image.version="build_main"
VIASHDOCKER

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

@@ -430,7 +430,7 @@ build_info:
output: "target/executable/mapping/spaceranger_count"
executable: "target/executable/mapping/spaceranger_count/spaceranger_count"
viash_version: "0.9.4"
git_commit: "280b21fc21238c6e7b2e76089deffdef5d979b34"
git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
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="2025-07-24T15:22:52Z"
LABEL org.opencontainers.image.created="2025-08-18T07:54:17Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="280b21fc21238c6e7b2e76089deffdef5d979b34"
LABEL org.opencontainers.image.revision="226d7de695d56f116dd1ba8e08a51ebf63b153b3"
LABEL org.opencontainers.image.version="build_main"
VIASHDOCKER

11
target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml
View File

@@ -198,8 +198,13 @@ engines:
- type: "python"
user: false
packages:
- "squidpy~=1.6.5"
- "anndata~=0.11.1"
- "mudata~=0.3.1"
- "spatialdata~=0.4.1rc"
- "squidpy~=1.6.5"
script:
- "exec(\"try:\\n import awkward\\nexcept ModuleNotFoundError:\\n exit(0)\\\
nelse: exit(1)\")"
upgrade: true
test_setup:
- type: "apt"
@@ -209,7 +214,7 @@ engines:
- type: "python"
user: false
packages:
- "viashpy==0.8.0"
- "viashpy==0.9.0"
github:
- "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
upgrade: true
@@ -224,7 +229,7 @@ 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: "280b21fc21238c6e7b2e76089deffdef5d979b34"
git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

13
target/nextflow/convert/from_cosmx_to_h5mu/main.nf
View File

@@ -3294,8 +3294,13 @@ meta = [
"type" : "python",
"user" : false,
"packages" : [
"squidpy~=1.6.5",
"mudata~=0.3.1"
"anndata~=0.11.1",
"mudata~=0.3.1",
"spatialdata~=0.4.1rc",
"squidpy~=1.6.5"
],
"script" : [
"exec(\\"try:\\\\n import awkward\\\\nexcept ModuleNotFoundError:\\\\n exit(0)\\\\nelse: exit(1)\\")"
],
"upgrade" : true
}
@@ -3312,7 +3317,7 @@ meta = [
"type" : "python",
"user" : false,
"packages" : [
"viashpy==0.8.0"
"viashpy==0.9.0"
],
"github" : [
"openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
@@ -3332,7 +3337,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_h5mu",
"viash_version" : "0.9.4",
"git_commit" : "280b21fc21238c6e7b2e76089deffdef5d979b34",
"git_commit" : "226d7de695d56f116dd1ba8e08a51ebf63b153b3",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

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

@@ -236,7 +236,7 @@ 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: "280b21fc21238c6e7b2e76089deffdef5d979b34"
git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

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

@@ -3328,7 +3328,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_spatialexperiment",
"viash_version" : "0.9.4",
"git_commit" : "280b21fc21238c6e7b2e76089deffdef5d979b34",
"git_commit" : "226d7de695d56f116dd1ba8e08a51ebf63b153b3",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {
@@ -3430,7 +3430,7 @@ rm(.viash_orig_warn)
### VIASH END
if (par\\$add_polygon_path == FALSE & par\\$add_tx_path == FALSE) {
if (par\\$add_polygon_path == FALSE && par\\$add_tx_path == FALSE) {
add_parquet_paths <- FALSE
} else {
add_parquet_paths <- TRUE

11
target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
View File

@@ -194,9 +194,12 @@ engines:
- type: "python"
user: false
packages:
- "spatialdata~=0.4.0"
- "spatialdata-io~=0.2.0"
- "anndata~=0.11.1"
- "mudata~=0.3.1"
- "spatialdata~=0.4.1rc"
script:
- "exec(\"try:\\n import awkward\\nexcept ModuleNotFoundError:\\n exit(0)\\\
nelse: exit(1)\")"
upgrade: true
test_setup:
- type: "apt"
@@ -206,7 +209,7 @@ engines:
- type: "python"
user: false
packages:
- "viashpy==0.8.0"
- "viashpy==0.9.0"
github:
- "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
upgrade: true
@@ -221,7 +224,7 @@ 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: "280b21fc21238c6e7b2e76089deffdef5d979b34"
git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

13
target/nextflow/convert/from_spatialdata_to_h5mu/main.nf
View File

@@ -3294,9 +3294,12 @@ meta = [
"type" : "python",
"user" : false,
"packages" : [
"spatialdata~=0.4.0",
"spatialdata-io~=0.2.0",
"mudata~=0.3.1"
"anndata~=0.11.1",
"mudata~=0.3.1",
"spatialdata~=0.4.1rc"
],
"script" : [
"exec(\\"try:\\\\n import awkward\\\\nexcept ModuleNotFoundError:\\\\n exit(0)\\\\nelse: exit(1)\\")"
],
"upgrade" : true
}
@@ -3313,7 +3316,7 @@ meta = [
"type" : "python",
"user" : false,
"packages" : [
"viashpy==0.8.0"
"viashpy==0.9.0"
],
"github" : [
"openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
@@ -3333,7 +3336,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_spatialdata_to_h5mu",
"viash_version" : "0.9.4",
"git_commit" : "280b21fc21238c6e7b2e76089deffdef5d979b34",
"git_commit" : "226d7de695d56f116dd1ba8e08a51ebf63b153b3",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

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

@@ -292,7 +292,8 @@ engines:
- type: "python"
user: false
packages:
- "spatialdata-io~=0.1.7"
- "spatialdata~=0.4.1rc"
- "spatialdata-io~=0.2.0"
upgrade: true
test_setup:
- type: "apt"
@@ -302,8 +303,7 @@ engines:
- type: "python"
user: false
packages:
- "viashpy==0.8.0"
- "spatialdata~=0.3.0"
- "viashpy==0.9.0"
github:
- "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
upgrade: true
@@ -318,7 +318,7 @@ build_info:
output: "target/nextflow/convert/from_xenium_to_spatialdata"
executable: "target/nextflow/convert/from_xenium_to_spatialdata/main.nf"
viash_version: "0.9.4"
git_commit: "280b21fc21238c6e7b2e76089deffdef5d979b34"
git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

8
target/nextflow/convert/from_xenium_to_spatialdata/main.nf
View File

@@ -3393,7 +3393,8 @@ meta = [
"type" : "python",
"user" : false,
"packages" : [
"spatialdata-io~=0.1.7"
"spatialdata~=0.4.1rc",
"spatialdata-io~=0.2.0"
],
"upgrade" : true
}
@@ -3410,8 +3411,7 @@ meta = [
"type" : "python",
"user" : false,
"packages" : [
"viashpy==0.8.0",
"spatialdata~=0.3.0"
"viashpy==0.9.0"
],
"github" : [
"openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
@@ -3431,7 +3431,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialdata",
"viash_version" : "0.9.4",
"git_commit" : "280b21fc21238c6e7b2e76089deffdef5d979b34",
"git_commit" : "226d7de695d56f116dd1ba8e08a51ebf63b153b3",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

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

@@ -226,7 +226,7 @@ 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: "280b21fc21238c6e7b2e76089deffdef5d979b34"
git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
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

@@ -3317,7 +3317,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialexperiment",
"viash_version" : "0.9.4",
"git_commit" : "280b21fc21238c6e7b2e76089deffdef5d979b34",
"git_commit" : "226d7de695d56f116dd1ba8e08a51ebf63b153b3",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

5
target/nextflow/filter/subset_cosmx/.config.vsh.yaml
View File

@@ -205,6 +205,7 @@ engines:
- type: "python"
user: false
packages:
- "spatialdata~=0.4.1rc"
- "squidpy~=1.6.5"
upgrade: true
test_setup:
@@ -215,7 +216,7 @@ engines:
- type: "python"
user: false
packages:
- "viashpy==0.8.0"
- "viashpy==0.9.0"
github:
- "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
upgrade: true
@@ -230,7 +231,7 @@ build_info:
output: "target/nextflow/filter/subset_cosmx"
executable: "target/nextflow/filter/subset_cosmx/main.nf"
viash_version: "0.9.4"
git_commit: "280b21fc21238c6e7b2e76089deffdef5d979b34"
git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

5
target/nextflow/filter/subset_cosmx/main.nf
View File

@@ -3301,6 +3301,7 @@ meta = [
"type" : "python",
"user" : false,
"packages" : [
"spatialdata~=0.4.1rc",
"squidpy~=1.6.5"
],
"upgrade" : true
@@ -3318,7 +3319,7 @@ meta = [
"type" : "python",
"user" : false,
"packages" : [
"viashpy==0.8.0"
"viashpy==0.9.0"
],
"github" : [
"openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
@@ -3338,7 +3339,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/filter/subset_cosmx",
"viash_version" : "0.9.4",
"git_commit" : "280b21fc21238c6e7b2e76089deffdef5d979b34",
"git_commit" : "226d7de695d56f116dd1ba8e08a51ebf63b153b3",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

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

@@ -430,7 +430,7 @@ build_info:
output: "target/nextflow/mapping/spaceranger_count"
executable: "target/nextflow/mapping/spaceranger_count/main.nf"
viash_version: "0.9.4"
git_commit: "280b21fc21238c6e7b2e76089deffdef5d979b34"
git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

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

@@ -3554,7 +3554,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/mapping/spaceranger_count",
"viash_version" : "0.9.4",
"git_commit" : "280b21fc21238c6e7b2e76089deffdef5d979b34",
"git_commit" : "226d7de695d56f116dd1ba8e08a51ebf63b153b3",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

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

@@ -648,7 +648,7 @@ 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: "280b21fc21238c6e7b2e76089deffdef5d979b34"
git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
dependencies:
- "target/dependencies/github/openpipelines-bio/openpipeline/disable-scrublet_build/nextflow/workflows/multiomics/process_samples"

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

@@ -3819,7 +3819,7 @@ meta = [
"engine" : "native",
"output" : "/workdir/root/repo/target/nextflow/workflows/multiomics/spatial_process_samples",
"viash_version" : "0.9.4",
"git_commit" : "280b21fc21238c6e7b2e76089deffdef5d979b34",
"git_commit" : "226d7de695d56f116dd1ba8e08a51ebf63b153b3",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

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

@@ -391,7 +391,7 @@ 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: "280b21fc21238c6e7b2e76089deffdef5d979b34"
git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
dependencies:
- "target/dependencies/github/openpipelines-bio/openpipeline/2.1.2/nextflow/workflows/qc/qc"

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

@@ -3511,7 +3511,7 @@ meta = [
"engine" : "native",
"output" : "/workdir/root/repo/target/nextflow/workflows/qc/spatial_qc",
"viash_version" : "0.9.4",
"git_commit" : "280b21fc21238c6e7b2e76089deffdef5d979b34",
"git_commit" : "226d7de695d56f116dd1ba8e08a51ebf63b153b3",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {