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Build branch openpipeline_spatial/niche-compass with version niche-compass to openpipeline_spatial on branch niche-compass (f91eceb)

Browse Source 
Build pipeline: openpipelines-bio.openpipeline-spatial.niche-compass-9r6kv

Source commit: f91eceb7cf

Source message: use cuda if available
This commit is contained in:
CI
2026-01-26 09:58:49 +00:00
parent 79cf7a614d
commit 5304c707b7
63 changed files with 82 additions and 94 deletions
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8
src/nichecompass/nichecompass/script.py
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@@ -4,7 +4,6 @@ import mudata as mu
from nichecompass.models import NicheCompass
from nichecompass.utils import add_gps_from_gp_dict_to_adata
from torch.cuda import is_available as cuda_is_available
## VIASH START
par = {
@@ -92,9 +91,6 @@ from setup_logger import setup_logger
logger = setup_logger()
use_gpu = cuda_is_available()
logger.info("GPU enabled? %s", use_gpu)
## Read in data
adata = mu.read_h5ad(par["input"], mod=par["modality"])
@@ -175,7 +171,7 @@ model = NicheCompass(
n_addon_gp=par["n_addon_gp"],
cat_covariates_embeds_nums=par["cat_covariates_embeds_nums"],
seed=par["random_state"],
use_cuda_if_available=use_gpu,
use_cuda_if_available=True,
)
logger.info("Training NicheCompass model...")
@@ -203,7 +199,7 @@ model.train(
edge_batch_size=par["edge_batch_size"],
node_batch_size=par["node_batch_size"],
n_sampled_neighbors=par["n_sampled_neighbors"],
use_cuda_if_available=use_gpu,
use_cuda_if_available=True,
)
## Save model and data

2
target/_private/executable/filter/subset_cosmx/.config.vsh.yaml
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@@ -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: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/_private/executable/filter/subset_cosmx/subset_cosmx
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@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz"
LABEL org.opencontainers.image.description="Companion container for running component filter subset_cosmx"
LABEL org.opencontainers.image.created="2026-01-21T10:40:04Z"
LABEL org.opencontainers.image.created="2026-01-26T08:53:43Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
LABEL org.opencontainers.image.version="niche-compass"
VIASHDOCKER

2
target/_private/nextflow/filter/subset_cosmx/.config.vsh.yaml
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@@ -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: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

2
target/_private/nextflow/filter/subset_cosmx/main.nf
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@@ -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" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
"git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

2
target/_test/executable/test_workflows/niche/nichecompass_leiden_test/.config.vsh.yaml
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@@ -154,7 +154,7 @@ 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: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
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
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@@ -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="2026-01-21T10:40:03Z"
LABEL org.opencontainers.image.created="2026-01-26T08:53:42Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
LABEL org.opencontainers.image.version="niche-compass"
VIASHDOCKER

2
target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/.config.vsh.yaml
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@@ -154,7 +154,7 @@ 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: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
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
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@@ -3234,7 +3234,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test",
"viash_version" : "0.9.4",
"git_commit" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
"git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

2
target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml
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@@ -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: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
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
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@@ -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="2026-01-21T10:40:04Z"
LABEL org.opencontainers.image.created="2026-01-26T08:53:43Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
LABEL org.opencontainers.image.version="niche-compass"
VIASHDOCKER

2
target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml
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@@ -238,7 +238,7 @@ 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: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu
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@@ -460,9 +460,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz"
LABEL org.opencontainers.image.description="Companion container for running component convert from_cosmx_to_h5mu"
LABEL org.opencontainers.image.created="2026-01-21T10:40:03Z"
LABEL org.opencontainers.image.created="2026-01-26T08:53:42Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
LABEL org.opencontainers.image.version="niche-compass"
VIASHDOCKER

2
target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml
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@@ -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: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
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
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@@ -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="2026-01-21T10:40:02Z"
LABEL org.opencontainers.image.created="2026-01-26T08:53:41Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
LABEL org.opencontainers.image.version="niche-compass"
VIASHDOCKER

2
target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml
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@@ -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: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
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
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@@ -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="2026-01-21T10:40:04Z"
LABEL org.opencontainers.image.created="2026-01-26T08:53:43Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
LABEL org.opencontainers.image.version="niche-compass"
VIASHDOCKER

2
target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
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@@ -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: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu
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@@ -459,9 +459,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz"
LABEL org.opencontainers.image.description="Companion container for running component convert from_spatialdata_to_h5mu"
LABEL org.opencontainers.image.created="2026-01-21T10:40:03Z"
LABEL org.opencontainers.image.created="2026-01-26T08:53:42Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
LABEL org.opencontainers.image.version="niche-compass"
VIASHDOCKER

2
target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml
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@@ -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: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
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
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@@ -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="2026-01-21T10:40:03Z"
LABEL org.opencontainers.image.created="2026-01-26T08:53:42Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
LABEL org.opencontainers.image.version="niche-compass"
VIASHDOCKER

2
target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml
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@@ -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: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
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
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@@ -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="2026-01-21T10:40:04Z"
LABEL org.opencontainers.image.created="2026-01-26T08:53:43Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
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: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
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="2026-01-21T10:40:03Z"
LABEL org.opencontainers.image.created="2026-01-26T08:53:42Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
LABEL org.opencontainers.image.version="niche-compass"
VIASHDOCKER

2
target/executable/dataflow/concatenate_h5mu/.config.vsh.yaml
View File

@@ -302,7 +302,7 @@ build_info:
output: "target/executable/dataflow/concatenate_h5mu"
executable: "target/executable/dataflow/concatenate_h5mu/concatenate_h5mu"
viash_version: "0.9.4"
git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/executable/dataflow/concatenate_h5mu/concatenate_h5mu
View File

@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont"
LABEL org.opencontainers.image.description="Companion container for running component dataflow concatenate_h5mu"
LABEL org.opencontainers.image.created="2026-01-21T10:40:04Z"
LABEL org.opencontainers.image.created="2026-01-26T08:53:43Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
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: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
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="2026-01-21T10:40:03Z"
LABEL org.opencontainers.image.created="2026-01-26T08:53:42Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
LABEL org.opencontainers.image.version="niche-compass"
VIASHDOCKER

2
target/executable/neighbors/spatial_neighborhood_graph/.config.vsh.yaml
View File

@@ -269,7 +269,7 @@ 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: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/executable/neighbors/spatial_neighborhood_graph/spatial_neighborhood_graph
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 neighbors spatial_neighborhood_graph"
LABEL org.opencontainers.image.created="2026-01-21T10:40:03Z"
LABEL org.opencontainers.image.created="2026-01-26T08:53:42Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
LABEL org.opencontainers.image.version="niche-compass"
VIASHDOCKER

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

@@ -1003,7 +1003,7 @@ build_info:
output: "target/executable/nichecompass/nichecompass"
executable: "target/executable/nichecompass/nichecompass/nichecompass"
viash_version: "0.9.4"
git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

12
target/executable/nichecompass/nichecompass/nichecompass
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@@ -464,9 +464,9 @@ 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="2026-01-21T10:40:02Z"
LABEL org.opencontainers.image.created="2026-01-26T08:53:41Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="367d72e60cef484c48083ac3f0abc8f81fa2378f"
LABEL org.opencontainers.image.revision="f91eceb7cf408169b2847c359c6e2acd77856ff7"
LABEL org.opencontainers.image.version="niche-compass"
VIASHDOCKER
@@ -3115,7 +3115,6 @@ import mudata as mu
from nichecompass.models import NicheCompass
from nichecompass.utils import add_gps_from_gp_dict_to_adata
from torch.cuda import is_available as cuda_is_available
## VIASH START
# The following code has been auto-generated by Viash.
@@ -3221,9 +3220,6 @@ from setup_logger import setup_logger
logger = setup_logger()
use_gpu = cuda_is_available()
logger.info("GPU enabled? %s", use_gpu)
## Read in data
adata = mu.read_h5ad(par["input"], mod=par["modality"])
@@ -3304,7 +3300,7 @@ model = NicheCompass(
n_addon_gp=par["n_addon_gp"],
cat_covariates_embeds_nums=par["cat_covariates_embeds_nums"],
seed=par["random_state"],
use_cuda_if_available=use_gpu,
use_cuda_if_available=True,
)
logger.info("Training NicheCompass model...")
@@ -3332,7 +3328,7 @@ model.train(
edge_batch_size=par["edge_batch_size"],
node_batch_size=par["node_batch_size"],
n_sampled_neighbors=par["n_sampled_neighbors"],
use_cuda_if_available=use_gpu,
use_cuda_if_available=True,
)
## Save model and data

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

@@ -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: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
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

@@ -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" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
"git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

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

@@ -238,7 +238,7 @@ 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: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

2
target/nextflow/convert/from_cosmx_to_h5mu/main.nf
View File

@@ -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" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
"git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
"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: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
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" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
"git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

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

@@ -224,7 +224,7 @@ build_info:
output: "target/nextflow/convert/from_h5mu_to_spatialexperiment"
executable: "target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf"
viash_version: "0.9.4"
git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

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

@@ -3332,7 +3332,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_h5mu_to_spatialexperiment",
"viash_version" : "0.9.4",
"git_commit" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
"git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

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

@@ -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: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

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

@@ -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" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
"git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

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

@@ -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: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
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

@@ -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" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
"git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
"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: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
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" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
"git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
"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: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
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" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
"git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

2
target/nextflow/dataflow/concatenate_h5mu/.config.vsh.yaml
View File

@@ -302,7 +302,7 @@ build_info:
output: "target/nextflow/dataflow/concatenate_h5mu"
executable: "target/nextflow/dataflow/concatenate_h5mu/main.nf"
viash_version: "0.9.4"
git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

2
target/nextflow/dataflow/concatenate_h5mu/main.nf
View File

@@ -3399,7 +3399,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/dataflow/concatenate_h5mu",
"viash_version" : "0.9.4",
"git_commit" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
"git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
"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: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
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" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
"git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

2
target/nextflow/neighbors/spatial_neighborhood_graph/.config.vsh.yaml
View File

@@ -269,7 +269,7 @@ 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: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

2
target/nextflow/neighbors/spatial_neighborhood_graph/main.nf
View File

@@ -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" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
"git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

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

@@ -1003,7 +1003,7 @@ build_info:
output: "target/nextflow/nichecompass/nichecompass"
executable: "target/nextflow/nichecompass/nichecompass/main.nf"
viash_version: "0.9.4"
git_commit: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

10
target/nextflow/nichecompass/nichecompass/main.nf
View File

@@ -4138,7 +4138,7 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/nichecompass/nichecompass",
"viash_version" : "0.9.4",
"git_commit" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
"git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {
@@ -4194,7 +4194,6 @@ import mudata as mu
from nichecompass.models import NicheCompass
from nichecompass.utils import add_gps_from_gp_dict_to_adata
from torch.cuda import is_available as cuda_is_available
## VIASH START
# The following code has been auto-generated by Viash.
@@ -4300,9 +4299,6 @@ from setup_logger import setup_logger
logger = setup_logger()
use_gpu = cuda_is_available()
logger.info("GPU enabled? %s", use_gpu)
## Read in data
adata = mu.read_h5ad(par["input"], mod=par["modality"])
@@ -4383,7 +4379,7 @@ model = NicheCompass(
n_addon_gp=par["n_addon_gp"],
cat_covariates_embeds_nums=par["cat_covariates_embeds_nums"],
seed=par["random_state"],
use_cuda_if_available=use_gpu,
use_cuda_if_available=True,
)
logger.info("Training NicheCompass model...")
@@ -4411,7 +4407,7 @@ model.train(
edge_batch_size=par["edge_batch_size"],
node_batch_size=par["node_batch_size"],
n_sampled_neighbors=par["n_sampled_neighbors"],
use_cuda_if_available=use_gpu,
use_cuda_if_available=True,
)
## Save model and data

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: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
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" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
"git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {

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

@@ -795,7 +795,7 @@ 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: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
dependencies:
- "target/nextflow/dataflow/concatenate_h5mu"

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

@@ -3948,7 +3948,7 @@ meta = [
"engine" : "native",
"output" : "/workdir/root/repo/target/nextflow/workflows/niche/nichecompass_leiden",
"viash_version" : "0.9.4",
"git_commit" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
"git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
"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: "367d72e60cef484c48083ac3f0abc8f81fa2378f"
git_commit: "f91eceb7cf408169b2847c359c6e2acd77856ff7"
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" : "367d72e60cef484c48083ac3f0abc8f81fa2378f",
"git_commit" : "f91eceb7cf408169b2847c359c6e2acd77856ff7",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {