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

Build branch openpipeline_spatial/niche-compass with version niche-compass to openpipeline_spatial on branch niche-compass (c5caee7)

Browse Source 
Build pipeline: openpipelines-bio.openpipeline-spatial.niche-compass-6glnt

Source commit: c5caee72d5

Source message: Merge remote-tracking branch 'origin/update-spatialdata' into niche-compass
This commit is contained in:
CI
2026-02-16 09:59:54 +00:00
parent 0c1b5c1ac9
commit 9882fd15d5
71 changed files with 112 additions and 106 deletions
Download Patch File Download Diff File Expand all files Collapse all files

6
CHANGELOG.md
View File

@@ -1,3 +1,9 @@
# openpipeline_spatial x.x.x
## MINOR CHANGES
* Bump squidpy to 1.8.1 and spatialdata to 0.7.2 (PR #41).
# openpipeline_spatial 0.2.0
## NEW FUNCTIONALITY

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

@@ -1,3 +1,3 @@
packages:
- spatialdata~=0.6.1
- spatialdata~=0.7.2
- pyarrow~=18.0.0

4
src/base/requirements/squidpy.yaml
View File

@@ -1,4 +1,4 @@
__merge__: [/src/base/requirements/spatialdata.yaml, .]
packages:
- squidpy~=1.7.0
__merge__: [/src/base/requirements/scanpy.yaml, .]
- squidpy~=1.8.1
__merge__: [/src/base/requirements/scanpy.yaml, .]

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

@@ -202,7 +202,7 @@ engines:
user: false
packages:
- "scanpy~=1.10.4"
- "squidpy~=1.7.0"
- "squidpy~=1.8.1"
upgrade: true
test_setup:
- type: "apt"
@@ -227,7 +227,7 @@ 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: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
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 "scanpy~=1.10.4" "squidpy~=1.7.0"
pip install --upgrade --no-cache-dir "scanpy~=1.10.4" "squidpy~=1.8.1"
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="2026-01-27T10:47:56Z"
LABEL org.opencontainers.image.created="2026-02-16T09:01:54Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="a4d81924a673566026c204c55add247504ef1c56"
LABEL org.opencontainers.image.revision="c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
LABEL org.opencontainers.image.version="niche-compass"
VIASHDOCKER

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

@@ -202,7 +202,7 @@ engines:
user: false
packages:
- "scanpy~=1.10.4"
- "squidpy~=1.7.0"
- "squidpy~=1.8.1"
upgrade: true
test_setup:
- type: "apt"
@@ -227,7 +227,7 @@ 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: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
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

@@ -3296,7 +3296,7 @@ meta = [
"user" : false,
"packages" : [
"scanpy~=1.10.4",
"squidpy~=1.7.0"
"squidpy~=1.8.1"
],
"upgrade" : true
}
@@ -3333,7 +3333,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/_private/nextflow/filter/subset_cosmx",
"viash_version" : "0.9.4",
"git_commit" : "a4d81924a673566026c204c55add247504ef1c56",
"git_commit" : "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

2
target/_test/executable/test_workflows/ingestion/spaceranger_mapping_test/.config.vsh.yaml
View File

@@ -157,7 +157,7 @@ build_info:
output: "target/_test/executable/test_workflows/ingestion/spaceranger_mapping_test"
executable: "target/_test/executable/test_workflows/ingestion/spaceranger_mapping_test/spaceranger_mapping_test"
viash_version: "0.9.4"
git_commit: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/_test/executable/test_workflows/ingestion/spaceranger_mapping_test/spaceranger_mapping_test
View File

@@ -459,9 +459,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dorien Roosen"
LABEL org.opencontainers.image.description="Companion container for running component test_workflows/ingestion spaceranger_mapping_test"
LABEL org.opencontainers.image.created="2026-01-27T10:47:55Z"
LABEL org.opencontainers.image.created="2026-02-16T09:01:53Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="a4d81924a673566026c204c55add247504ef1c56"
LABEL org.opencontainers.image.revision="c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
LABEL org.opencontainers.image.version="niche-compass"
VIASHDOCKER

2
target/_test/executable/test_workflows/niche/nichecompass_leiden_test/.config.vsh.yaml
View File

@@ -156,7 +156,7 @@ build_info:
output: "target/_test/executable/test_workflows/niche/nichecompass_leiden_test"
executable: "target/_test/executable/test_workflows/niche/nichecompass_leiden_test/nichecompass_leiden_test"
viash_version: "0.9.4"
git_commit: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/_test/executable/test_workflows/niche/nichecompass_leiden_test/nichecompass_leiden_test
View File

@@ -459,9 +459,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dorien Roosen"
LABEL org.opencontainers.image.description="Companion container for running component test_workflows/niche nichecompass_leiden_test"
LABEL org.opencontainers.image.created="2026-01-27T10:47:55Z"
LABEL org.opencontainers.image.created="2026-02-16T09:01:53Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="a4d81924a673566026c204c55add247504ef1c56"
LABEL org.opencontainers.image.revision="c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
LABEL org.opencontainers.image.version="niche-compass"
VIASHDOCKER

2
target/_test/nextflow/test_workflows/ingestion/spaceranger_mapping_test/.config.vsh.yaml
View File

@@ -157,7 +157,7 @@ build_info:
output: "target/_test/nextflow/test_workflows/ingestion/spaceranger_mapping_test"
executable: "target/_test/nextflow/test_workflows/ingestion/spaceranger_mapping_test/main.nf"
viash_version: "0.9.4"
git_commit: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

2
target/_test/nextflow/test_workflows/ingestion/spaceranger_mapping_test/main.nf
View File

@@ -3235,7 +3235,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/ingestion/spaceranger_mapping_test",
"viash_version" : "0.9.4",
"git_commit" : "a4d81924a673566026c204c55add247504ef1c56",
"git_commit" : "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

2
target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/.config.vsh.yaml
View File

@@ -156,7 +156,7 @@ build_info:
output: "target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test"
executable: "target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/main.nf"
viash_version: "0.9.4"
git_commit: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

2
target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/main.nf
View File

@@ -3235,7 +3235,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test",
"viash_version" : "0.9.4",
"git_commit" : "a4d81924a673566026c204c55add247504ef1c56",
"git_commit" : "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

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

@@ -303,7 +303,7 @@ 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: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu
View File

@@ -459,9 +459,9 @@ 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="2026-01-27T10:47:56Z"
LABEL org.opencontainers.image.created="2026-02-16T09:01:55Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="a4d81924a673566026c204c55add247504ef1c56"
LABEL org.opencontainers.image.revision="c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
LABEL org.opencontainers.image.version="niche-compass"
VIASHDOCKER

4
target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml
View File

@@ -203,7 +203,7 @@ engines:
- "awkward"
- "mudata~=0.3.2"
- "scanpy~=1.10.4"
- "squidpy~=1.7.0"
- "squidpy~=1.8.1"
- "pyarrow"
git:
- "https://codeberg.org/miurahr/zipfile-inflate64.git@v0.2"
@@ -239,7 +239,7 @@ 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: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

6
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~=0.12.7" "awkward" "mudata~=0.3.2" "scanpy~=1.10.4" "squidpy~=1.7.0" "pyarrow" && \
pip install --upgrade --no-cache-dir "anndata~=0.12.7" "awkward" "mudata~=0.3.2" "scanpy~=1.10.4" "squidpy~=1.8.1" "pyarrow" && \
pip install --upgrade --no-cache-dir "git+https://codeberg.org/miurahr/zipfile-inflate64.git@v0.2" && \
python -c 'exec("try:\n import zarr; from importlib.metadata import version\nexcept ModuleNotFoundError:\n exit(0)\nelse: assert int(version(\"zarr\").partition(\".\")[0]) > 2")'
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="2026-01-27T10:47:54Z"
LABEL org.opencontainers.image.created="2026-02-16T09:01:52Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="a4d81924a673566026c204c55add247504ef1c56"
LABEL org.opencontainers.image.revision="c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
LABEL org.opencontainers.image.version="niche-compass"
VIASHDOCKER

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: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
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="2026-01-27T10:47:54Z"
LABEL org.opencontainers.image.created="2026-02-16T09:01:53Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="a4d81924a673566026c204c55add247504ef1c56"
LABEL org.opencontainers.image.revision="c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
LABEL org.opencontainers.image.version="niche-compass"
VIASHDOCKER

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

@@ -227,7 +227,7 @@ 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: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
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="2026-01-27T10:47:55Z"
LABEL org.opencontainers.image.created="2026-02-16T09:01:54Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="a4d81924a673566026c204c55add247504ef1c56"
LABEL org.opencontainers.image.revision="c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
LABEL org.opencontainers.image.version="niche-compass"
VIASHDOCKER

2
target/executable/convert/from_spaceranger_to_h5mu/.config.vsh.yaml
View File

@@ -265,7 +265,7 @@ build_info:
output: "target/executable/convert/from_spaceranger_to_h5mu"
executable: "target/executable/convert/from_spaceranger_to_h5mu/from_spaceranger_to_h5mu"
viash_version: "0.9.4"
git_commit: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/executable/convert/from_spaceranger_to_h5mu/from_spaceranger_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_spaceranger_to_h5mu"
LABEL org.opencontainers.image.created="2026-01-27T10:47:54Z"
LABEL org.opencontainers.image.created="2026-02-16T09:01:54Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="a4d81924a673566026c204c55add247504ef1c56"
LABEL org.opencontainers.image.revision="c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
LABEL org.opencontainers.image.version="niche-compass"
VIASHDOCKER

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

@@ -193,7 +193,7 @@ engines:
- "anndata~=0.12.7"
- "awkward"
- "mudata~=0.3.2"
- "spatialdata~=0.6.1"
- "spatialdata~=0.7.2"
- "pyarrow~=18.0.0"
script:
- "exec(\"try:\\n import zarr; from importlib.metadata import version\\nexcept\
@@ -223,7 +223,7 @@ 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: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
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~=0.12.7" "awkward" "mudata~=0.3.2" "spatialdata~=0.6.1" "pyarrow~=18.0.0" && \
pip install --upgrade --no-cache-dir "anndata~=0.12.7" "awkward" "mudata~=0.3.2" "spatialdata~=0.7.2" "pyarrow~=18.0.0" && \
python -c 'exec("try:\n import zarr; from importlib.metadata import version\nexcept ModuleNotFoundError:\n exit(0)\nelse: assert int(version(\"zarr\").partition(\".\")[0]) > 2")'
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="2026-01-27T10:47:55Z"
LABEL org.opencontainers.image.created="2026-02-16T09:01:54Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="a4d81924a673566026c204c55add247504ef1c56"
LABEL org.opencontainers.image.revision="c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
LABEL org.opencontainers.image.version="niche-compass"
VIASHDOCKER

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

@@ -246,7 +246,7 @@ 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: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu
View File

@@ -459,9 +459,9 @@ 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="2026-01-27T10:47:54Z"
LABEL org.opencontainers.image.created="2026-02-16T09:01:53Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="a4d81924a673566026c204c55add247504ef1c56"
LABEL org.opencontainers.image.revision="c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
LABEL org.opencontainers.image.version="niche-compass"
VIASHDOCKER

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

@@ -294,7 +294,7 @@ engines:
user: false
packages:
- "spatialdata-io~=0.5.1"
- "spatialdata~=0.6.1"
- "spatialdata~=0.7.2"
- "pyarrow~=18.0.0"
git:
- "https://codeberg.org/miurahr/zipfile-inflate64.git@v0.2"
@@ -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: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
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

@@ -454,14 +454,14 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "spatialdata-io~=0.5.1" "spatialdata~=0.6.1" "pyarrow~=18.0.0" && \
pip install --upgrade --no-cache-dir "spatialdata-io~=0.5.1" "spatialdata~=0.7.2" "pyarrow~=18.0.0" && \
pip install --upgrade --no-cache-dir "git+https://codeberg.org/miurahr/zipfile-inflate64.git@v0.2"
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="2026-01-27T10:47:55Z"
LABEL org.opencontainers.image.created="2026-02-16T09:01:53Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="a4d81924a673566026c204c55add247504ef1c56"
LABEL org.opencontainers.image.revision="c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
LABEL org.opencontainers.image.version="niche-compass"
VIASHDOCKER

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

@@ -238,7 +238,7 @@ 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: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
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

@@ -462,9 +462,9 @@ 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="2026-01-27T10:47:55Z"
LABEL org.opencontainers.image.created="2026-02-16T09:01:54Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="a4d81924a673566026c204c55add247504ef1c56"
LABEL org.opencontainers.image.revision="c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
LABEL org.opencontainers.image.version="niche-compass"
VIASHDOCKER

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

@@ -439,7 +439,7 @@ build_info:
output: "target/executable/mapping/spaceranger_count"
executable: "target/executable/mapping/spaceranger_count/spaceranger_count"
viash_version: "0.9.4"
git_commit: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
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="2026-01-27T10:47:54Z"
LABEL org.opencontainers.image.created="2026-02-16T09:01:52Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="a4d81924a673566026c204c55add247504ef1c56"
LABEL org.opencontainers.image.revision="c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
LABEL org.opencontainers.image.version="niche-compass"
VIASHDOCKER

4
target/executable/neighbors/spatial_neighborhood_graph/.config.vsh.yaml
View File

@@ -238,7 +238,7 @@ engines:
user: false
packages:
- "scanpy~=1.10.4"
- "squidpy~=1.7.0"
- "squidpy~=1.8.1"
- "anndata~=0.12.7"
- "awkward"
- "mudata~=0.3.2"
@@ -270,7 +270,7 @@ build_info:
output: "target/executable/neighbors/spatial_neighborhood_graph"
executable: "target/executable/neighbors/spatial_neighborhood_graph/spatial_neighborhood_graph"
viash_version: "0.9.4"
git_commit: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

6
target/executable/neighbors/spatial_neighborhood_graph/spatial_neighborhood_graph
View File

@@ -453,14 +453,14 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "scanpy~=1.10.4" "squidpy~=1.7.0" "anndata~=0.12.7" "awkward" "mudata~=0.3.2" && \
pip install --upgrade --no-cache-dir "scanpy~=1.10.4" "squidpy~=1.8.1" "anndata~=0.12.7" "awkward" "mudata~=0.3.2" && \
python -c 'exec("try:\n import zarr; from importlib.metadata import version\nexcept ModuleNotFoundError:\n exit(0)\nelse: assert int(version(\"zarr\").partition(\".\")[0]) > 2")'
LABEL org.opencontainers.image.authors="Dorien Roosen"
LABEL org.opencontainers.image.description="Companion container for running component neighbors spatial_neighborhood_graph"
LABEL org.opencontainers.image.created="2026-01-27T10:47:54Z"
LABEL org.opencontainers.image.created="2026-02-16T09:01:54Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="a4d81924a673566026c204c55add247504ef1c56"
LABEL org.opencontainers.image.revision="c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
LABEL org.opencontainers.image.version="niche-compass"
VIASHDOCKER

2
target/executable/nichecompass/nichecompass/.config.vsh.yaml
View File

@@ -998,7 +998,7 @@ build_info:
output: "target/executable/nichecompass/nichecompass"
executable: "target/executable/nichecompass/nichecompass/nichecompass"
viash_version: "0.9.4"
git_commit: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/executable/nichecompass/nichecompass/nichecompass
View File

@@ -460,9 +460,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dorien Roosen"
LABEL org.opencontainers.image.description="Companion container for running component nichecompass nichecompass"
LABEL org.opencontainers.image.created="2026-01-27T10:47:53Z"
LABEL org.opencontainers.image.created="2026-02-16T09:01:54Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="a4d81924a673566026c204c55add247504ef1c56"
LABEL org.opencontainers.image.revision="c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
LABEL org.opencontainers.image.version="niche-compass"
VIASHDOCKER

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

@@ -303,7 +303,7 @@ 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: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

2
target/nextflow/convert/from_cells2stats_to_h5mu/main.nf
View File

@@ -3400,7 +3400,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_cells2stats_to_h5mu",
"viash_version" : "0.9.4",
"git_commit" : "a4d81924a673566026c204c55add247504ef1c56",
"git_commit" : "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

4
target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml
View File

@@ -203,7 +203,7 @@ engines:
- "awkward"
- "mudata~=0.3.2"
- "scanpy~=1.10.4"
- "squidpy~=1.7.0"
- "squidpy~=1.8.1"
- "pyarrow"
git:
- "https://codeberg.org/miurahr/zipfile-inflate64.git@v0.2"
@@ -239,7 +239,7 @@ 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: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/nextflow/convert/from_cosmx_to_h5mu/main.nf
View File

@@ -3299,7 +3299,7 @@ meta = [
"awkward",
"mudata~=0.3.2",
"scanpy~=1.10.4",
"squidpy~=1.7.0",
"squidpy~=1.8.1",
"pyarrow"
],
"git" : [
@@ -3350,7 +3350,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_h5mu",
"viash_version" : "0.9.4",
"git_commit" : "a4d81924a673566026c204c55add247504ef1c56",
"git_commit" : "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

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: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
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" : "a4d81924a673566026c204c55add247504ef1c56",
"git_commit" : "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

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

@@ -227,7 +227,7 @@ 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: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
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

@@ -3334,7 +3334,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_h5mu_to_spatialexperiment",
"viash_version" : "0.9.4",
"git_commit" : "a4d81924a673566026c204c55add247504ef1c56",
"git_commit" : "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

2
target/nextflow/convert/from_spaceranger_to_h5mu/.config.vsh.yaml
View File

@@ -265,7 +265,7 @@ build_info:
output: "target/nextflow/convert/from_spaceranger_to_h5mu"
executable: "target/nextflow/convert/from_spaceranger_to_h5mu/main.nf"
viash_version: "0.9.4"
git_commit: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

2
target/nextflow/convert/from_spaceranger_to_h5mu/main.nf
View File

@@ -3368,7 +3368,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_spaceranger_to_h5mu",
"viash_version" : "0.9.4",
"git_commit" : "a4d81924a673566026c204c55add247504ef1c56",
"git_commit" : "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

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

@@ -193,7 +193,7 @@ engines:
- "anndata~=0.12.7"
- "awkward"
- "mudata~=0.3.2"
- "spatialdata~=0.6.1"
- "spatialdata~=0.7.2"
- "pyarrow~=18.0.0"
script:
- "exec(\"try:\\n import zarr; from importlib.metadata import version\\nexcept\
@@ -223,7 +223,7 @@ 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: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
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

@@ -3291,7 +3291,7 @@ meta = [
"anndata~=0.12.7",
"awkward",
"mudata~=0.3.2",
"spatialdata~=0.6.1",
"spatialdata~=0.7.2",
"pyarrow~=18.0.0"
],
"script" : [
@@ -3332,7 +3332,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_spatialdata_to_h5mu",
"viash_version" : "0.9.4",
"git_commit" : "a4d81924a673566026c204c55add247504ef1c56",
"git_commit" : "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

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

@@ -246,7 +246,7 @@ 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: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

2
target/nextflow/convert/from_xenium_to_h5mu/main.nf
View File

@@ -3349,7 +3349,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_h5mu",
"viash_version" : "0.9.4",
"git_commit" : "a4d81924a673566026c204c55add247504ef1c56",
"git_commit" : "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

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

@@ -294,7 +294,7 @@ engines:
user: false
packages:
- "spatialdata-io~=0.5.1"
- "spatialdata~=0.6.1"
- "spatialdata~=0.7.2"
- "pyarrow~=18.0.0"
git:
- "https://codeberg.org/miurahr/zipfile-inflate64.git@v0.2"
@@ -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: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

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

@@ -3395,7 +3395,7 @@ meta = [
"user" : false,
"packages" : [
"spatialdata-io~=0.5.1",
"spatialdata~=0.6.1",
"spatialdata~=0.7.2",
"pyarrow~=18.0.0"
],
"git" : [
@@ -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" : "a4d81924a673566026c204c55add247504ef1c56",
"git_commit" : "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

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

@@ -238,7 +238,7 @@ 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: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
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

@@ -3337,7 +3337,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialexperiment",
"viash_version" : "0.9.4",
"git_commit" : "a4d81924a673566026c204c55add247504ef1c56",
"git_commit" : "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

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

@@ -439,7 +439,7 @@ build_info:
output: "target/nextflow/mapping/spaceranger_count"
executable: "target/nextflow/mapping/spaceranger_count/main.nf"
viash_version: "0.9.4"
git_commit: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

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

@@ -3569,7 +3569,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/mapping/spaceranger_count",
"viash_version" : "0.9.4",
"git_commit" : "a4d81924a673566026c204c55add247504ef1c56",
"git_commit" : "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

4
target/nextflow/neighbors/spatial_neighborhood_graph/.config.vsh.yaml
View File

@@ -238,7 +238,7 @@ engines:
user: false
packages:
- "scanpy~=1.10.4"
- "squidpy~=1.7.0"
- "squidpy~=1.8.1"
- "anndata~=0.12.7"
- "awkward"
- "mudata~=0.3.2"
@@ -270,7 +270,7 @@ build_info:
output: "target/nextflow/neighbors/spatial_neighborhood_graph"
executable: "target/nextflow/neighbors/spatial_neighborhood_graph/main.nf"
viash_version: "0.9.4"
git_commit: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/nextflow/neighbors/spatial_neighborhood_graph/main.nf
View File

@@ -3330,7 +3330,7 @@ meta = [
"user" : false,
"packages" : [
"scanpy~=1.10.4",
"squidpy~=1.7.0",
"squidpy~=1.8.1",
"anndata~=0.12.7",
"awkward",
"mudata~=0.3.2"
@@ -3373,7 +3373,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/neighbors/spatial_neighborhood_graph",
"viash_version" : "0.9.4",
"git_commit" : "a4d81924a673566026c204c55add247504ef1c56",
"git_commit" : "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

2
target/nextflow/nichecompass/nichecompass/.config.vsh.yaml
View File

@@ -998,7 +998,7 @@ build_info:
output: "target/nextflow/nichecompass/nichecompass"
executable: "target/nextflow/nichecompass/nichecompass/main.nf"
viash_version: "0.9.4"
git_commit: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

2
target/nextflow/nichecompass/nichecompass/main.nf
View File

@@ -4129,7 +4129,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/nichecompass/nichecompass",
"viash_version" : "0.9.4",
"git_commit" : "a4d81924a673566026c204c55add247504ef1c56",
"git_commit" : "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

2
target/nextflow/workflows/ingestion/spaceranger_mapping/.config.vsh.yaml
View File

@@ -477,7 +477,7 @@ build_info:
output: "target/nextflow/workflows/ingestion/spaceranger_mapping"
executable: "target/nextflow/workflows/ingestion/spaceranger_mapping/main.nf"
viash_version: "0.9.4"
git_commit: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
dependencies:
- "target/nextflow/mapping/spaceranger_count"

2
target/nextflow/workflows/ingestion/spaceranger_mapping/main.nf
View File

@@ -3623,7 +3623,7 @@ meta = [
"engine" : "native",
"output" : "/workdir/root/repo/target/nextflow/workflows/ingestion/spaceranger_mapping",
"viash_version" : "0.9.4",
"git_commit" : "a4d81924a673566026c204c55add247504ef1c56",
"git_commit" : "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0",
"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: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
dependencies:
- "target/dependencies/vsh/vsh/openpipeline/v4.0.0/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" : "a4d81924a673566026c204c55add247504ef1c56",
"git_commit" : "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

2
target/nextflow/workflows/niche/nichecompass_leiden/.config.vsh.yaml
View File

@@ -797,7 +797,7 @@ build_info:
output: "target/nextflow/workflows/niche/nichecompass_leiden"
executable: "target/nextflow/workflows/niche/nichecompass_leiden/main.nf"
viash_version: "0.9.4"
git_commit: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
dependencies:
- "target/dependencies/vsh/vsh/openpipeline/v4.0.0/nextflow/dataflow/concatenate_h5mu"

2
target/nextflow/workflows/niche/nichecompass_leiden/main.nf
View File

@@ -3950,7 +3950,7 @@ meta = [
"engine" : "native",
"output" : "/workdir/root/repo/target/nextflow/workflows/niche/nichecompass_leiden",
"viash_version" : "0.9.4",
"git_commit" : "a4d81924a673566026c204c55add247504ef1c56",
"git_commit" : "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0",
"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: "a4d81924a673566026c204c55add247504ef1c56"
git_commit: "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
dependencies:
- "target/dependencies/vsh/vsh/openpipeline/v4.0.0/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" : "a4d81924a673566026c204c55add247504ef1c56",
"git_commit" : "c5caee72d51baeb9513607b3eeb1a22faf6b0ba0",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {