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‎src/workflows/annotation/scanvi_scarches/main.nf‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -113,7 +113,7 @@ workflow run_wf {
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"obsp_neighbor_connectivities": "scanvi_integration_connectivities",
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"obs_cluster": "scanvi_integration_leiden",
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"obsm_umap": "X_scanvi_umap"
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]
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],
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toState: [ "output": "output" ]
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)
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| setState(["output", "output_model"])

‎src/workflows/annotation/scanvi_scarches/test.nf‎

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Original file line numberDiff line numberDiff line change
@@ -52,6 +52,8 @@ workflow test_wf {
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"input": "output"
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]
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)
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output_ch
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| toSortedList({a, b -> a[0] <=> b[0]})
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| map { output_list ->
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assert output_list.size() == 1 : "output channel should contain 1 event"

‎src/workflows/test_workflows/annotation/scanvi_scarches/script.py‎

Lines changed: 8 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,10 @@ def test_run():
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input_mudata = read_h5mu(par["input"])
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expected_obsm = ["X_integrated_scanvi", "X_scanvi_umap"]
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expected_obs = ["scanvi_pred", "scanvi_probabilities"]
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expected_obsp = ["scanvi_integration_distances", "scanvi_integration_connectivities"]
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expected_obsp = [
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"scanvi_integration_distances",
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"scanvi_integration_connectivities",
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]
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expected_uns = ["scanvi_integration_neighbors"]
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assert "rna" in list(input_mudata.mod.keys()), "Input should contain rna modality."
@@ -32,8 +35,10 @@ def test_run():
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), f"Input mod['rna'] uns columns should be: {expected_uns}, found: {input_mudata.mod['rna'].uns.keys()}."
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assert input_mudata.mod["rna"].obs["scanvi_pred"].dtype == "category"
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assert pandas.api.types.is_float_dtype(input_mudata.mod["rna"].obs["scanvi_probabilities"].dtype)
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assert pandas.api.types.is_float_dtype(
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input_mudata.mod["rna"].obs["scanvi_probabilities"].dtype
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)
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if __name__ == "__main__":
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sys.exit(pytest.main(["--import-mode=importlib"]))
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sys.exit(pytest.main([__file__, "--import-mode=importlib"]))

‎target/executable/annotate/celltypist/.config.vsh.yaml‎

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@@ -416,9 +416,9 @@ build_info:
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output: "target/executable/annotate/celltypist"
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executable: "target/executable/annotate/celltypist/celltypist"
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viash_version: "0.9.3"
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git_commit: "87f6576dc12f1c9790a62ee6412242429e527fe5"
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git_commit: "26c00c397a3542af406bc6f366e785b5ac5c03f5"
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git_remote: "https://github.com/openpipelines-bio/openpipeline"
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git_tag: "2.0.0-rc.1-3-g87f6576dc12"
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git_tag: "2.0.0-rc.1-4-g26c00c397a3"
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package_config:
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name: "openpipeline"
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info:

‎target/executable/annotate/celltypist/celltypist‎

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Original file line numberDiff line numberDiff line change
@@ -465,9 +465,9 @@ RUN pip install --upgrade pip && \
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LABEL org.opencontainers.image.authors="Jakub Majercik, Weiwei Schultz"
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LABEL org.opencontainers.image.description="Companion container for running component annotate celltypist"
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LABEL org.opencontainers.image.created="2025-04-01T14:21:11Z"
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LABEL org.opencontainers.image.created="2025-04-02T07:57:08Z"
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LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
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LABEL org.opencontainers.image.revision="87f6576dc12f1c9790a62ee6412242429e527fe5"
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LABEL org.opencontainers.image.revision="26c00c397a3542af406bc6f366e785b5ac5c03f5"
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LABEL org.opencontainers.image.version="v2.1.0-rc.1"
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VIASHDOCKER

‎target/executable/annotate/onclass/.config.vsh.yaml‎

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@@ -387,9 +387,9 @@ build_info:
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output: "target/executable/annotate/onclass"
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executable: "target/executable/annotate/onclass/onclass"
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viash_version: "0.9.3"
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git_commit: "87f6576dc12f1c9790a62ee6412242429e527fe5"
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git_commit: "26c00c397a3542af406bc6f366e785b5ac5c03f5"
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git_remote: "https://github.com/openpipelines-bio/openpipeline"
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git_tag: "2.0.0-rc.1-3-g87f6576dc12"
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git_tag: "2.0.0-rc.1-4-g26c00c397a3"
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package_config:
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name: "openpipeline"
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info:

‎target/executable/annotate/onclass/onclass‎

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@@ -454,9 +454,9 @@ RUN pip install --upgrade pip && \
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LABEL org.opencontainers.image.authors="Jakub Majercik"
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LABEL org.opencontainers.image.description="Companion container for running component annotate onclass"
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LABEL org.opencontainers.image.created="2025-04-01T14:21:10Z"
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LABEL org.opencontainers.image.created="2025-04-02T07:57:08Z"
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LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
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LABEL org.opencontainers.image.revision="87f6576dc12f1c9790a62ee6412242429e527fe5"
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LABEL org.opencontainers.image.revision="26c00c397a3542af406bc6f366e785b5ac5c03f5"
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LABEL org.opencontainers.image.version="v2.1.0-rc.1"
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VIASHDOCKER

‎target/executable/annotate/popv/.config.vsh.yaml‎

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@@ -353,9 +353,9 @@ build_info:
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output: "target/executable/annotate/popv"
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executable: "target/executable/annotate/popv/popv"
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viash_version: "0.9.3"
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git_commit: "87f6576dc12f1c9790a62ee6412242429e527fe5"
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git_commit: "26c00c397a3542af406bc6f366e785b5ac5c03f5"
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git_remote: "https://github.com/openpipelines-bio/openpipeline"
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git_tag: "2.0.0-rc.1-3-g87f6576dc12"
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git_tag: "2.0.0-rc.1-4-g26c00c397a3"
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package_config:
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name: "openpipeline"
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info:

‎target/executable/annotate/popv/popv‎

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Original file line numberDiff line numberDiff line change
@@ -466,9 +466,9 @@ RUN cd /opt && git clone --depth 1 https://github.com/YosefLab/PopV.git
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LABEL org.opencontainers.image.authors="Matthias Beyens, Robrecht Cannoodt"
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LABEL org.opencontainers.image.description="Companion container for running component annotate popv"
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LABEL org.opencontainers.image.created="2025-04-01T14:21:10Z"
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LABEL org.opencontainers.image.created="2025-04-02T07:57:07Z"
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LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
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LABEL org.opencontainers.image.revision="87f6576dc12f1c9790a62ee6412242429e527fe5"
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LABEL org.opencontainers.image.revision="26c00c397a3542af406bc6f366e785b5ac5c03f5"
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LABEL org.opencontainers.image.version="v2.1.0-rc.1"
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VIASHDOCKER

‎target/executable/annotate/random_forest_annotation/.config.vsh.yaml‎

Lines changed: 2 additions & 2 deletions
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@@ -402,9 +402,9 @@ build_info:
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output: "target/executable/annotate/random_forest_annotation"
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executable: "target/executable/annotate/random_forest_annotation/random_forest_annotation"
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viash_version: "0.9.3"
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git_commit: "87f6576dc12f1c9790a62ee6412242429e527fe5"
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git_commit: "26c00c397a3542af406bc6f366e785b5ac5c03f5"
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git_remote: "https://github.com/openpipelines-bio/openpipeline"
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git_tag: "2.0.0-rc.1-3-g87f6576dc12"
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git_tag: "2.0.0-rc.1-4-g26c00c397a3"
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package_config:
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name: "openpipeline"
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info:

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