From b1ffb24eb918918bf277e5fbd663b093a0cb7235 Mon Sep 17 00:00:00 2001 From: CI Date: Mon, 18 Aug 2025 08:17:10 +0000 Subject: [PATCH] Build branch build/main with version build_main (226d7de) Build pipeline: openpipelines-bio.openpipeline-spatial.build-main-vdjx9 Source commit: https://github.com/openpipelines-bio/openpipeline_spatial/commit/226d7de695d56f116dd1ba8e08a51ebf63b153b3 Source message: deploy: 46b97b56724d241439f09d3748315a26f03a300d --- src/base/requirements/anndata.yaml | 2 ++ src/base/requirements/anndata_mudata.yaml | 5 +++++ src/base/requirements/openpipeline_testutils.yaml | 2 ++ src/base/requirements/python_test_setup.yaml | 8 ++++++++ src/base/requirements/scanpy.yaml | 2 ++ src/base/requirements/spatialdata-io.yaml | 3 +++ src/base/requirements/spatialdata.yaml | 2 ++ src/base/requirements/squidpy.yaml | 3 +++ src/base/requirements/viashpy.yaml | 2 ++ src/convert/from_cosmx_to_h5mu/config.vsh.yaml | 13 ++----------- .../from_cosmx_to_spatialexperiment/script.R | 6 ++++-- src/convert/from_cosmx_to_spatialexperiment/test.R | 12 +++++++++--- .../from_spatialdata_to_h5mu/config.vsh.yaml | 14 ++------------ .../from_xenium_to_spatialdata/config.vsh.yaml | 13 ++----------- .../from_xenium_to_spatialexperiment/script.R | 5 ++++- .../from_xenium_to_spatialexperiment/test.R | 11 ++++++++--- src/filter/subset_cosmx/config.vsh.yaml | 12 ++---------- .../convert/from_cosmx_to_h5mu/.config.vsh.yaml | 11 ++++++++--- .../convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu | 7 ++++--- .../.config.vsh.yaml | 2 +- .../from_cosmx_to_spatialexperiment | 6 +++--- .../from_spatialdata_to_h5mu/.config.vsh.yaml | 11 +++++++---- .../from_spatialdata_to_h5mu | 7 ++++--- .../from_xenium_to_spatialdata/.config.vsh.yaml | 8 ++++---- .../from_xenium_to_spatialdata | 6 +++--- .../.config.vsh.yaml | 2 +- .../from_xenium_to_spatialexperiment | 4 ++-- .../filter/subset_cosmx/.config.vsh.yaml | 5 +++-- target/executable/filter/subset_cosmx/subset_cosmx | 6 +++--- .../mapping/spaceranger_count/.config.vsh.yaml | 2 +- .../mapping/spaceranger_count/spaceranger_count | 4 ++-- .../convert/from_cosmx_to_h5mu/.config.vsh.yaml | 11 ++++++++--- target/nextflow/convert/from_cosmx_to_h5mu/main.nf | 13 +++++++++---- .../.config.vsh.yaml | 2 +- .../from_cosmx_to_spatialexperiment/main.nf | 4 ++-- .../from_spatialdata_to_h5mu/.config.vsh.yaml | 11 +++++++---- .../convert/from_spatialdata_to_h5mu/main.nf | 13 ++++++++----- .../from_xenium_to_spatialdata/.config.vsh.yaml | 8 ++++---- .../convert/from_xenium_to_spatialdata/main.nf | 8 ++++---- .../.config.vsh.yaml | 2 +- .../from_xenium_to_spatialexperiment/main.nf | 2 +- .../nextflow/filter/subset_cosmx/.config.vsh.yaml | 5 +++-- target/nextflow/filter/subset_cosmx/main.nf | 5 +++-- .../mapping/spaceranger_count/.config.vsh.yaml | 2 +- target/nextflow/mapping/spaceranger_count/main.nf | 2 +- .../spatial_process_samples/.config.vsh.yaml | 2 +- .../multiomics/spatial_process_samples/main.nf | 2 +- .../workflows/qc/spatial_qc/.config.vsh.yaml | 2 +- target/nextflow/workflows/qc/spatial_qc/main.nf | 2 +- 49 files changed, 165 insertions(+), 127 deletions(-) create mode 100644 src/base/requirements/anndata.yaml create mode 100644 src/base/requirements/anndata_mudata.yaml create mode 100644 src/base/requirements/openpipeline_testutils.yaml create mode 100644 src/base/requirements/python_test_setup.yaml create mode 100644 src/base/requirements/scanpy.yaml create mode 100644 src/base/requirements/spatialdata-io.yaml create mode 100644 src/base/requirements/spatialdata.yaml create mode 100644 src/base/requirements/squidpy.yaml create mode 100644 src/base/requirements/viashpy.yaml diff --git a/src/base/requirements/anndata.yaml b/src/base/requirements/anndata.yaml new file mode 100644 index 0000000..8ca4664 --- /dev/null +++ b/src/base/requirements/anndata.yaml @@ -0,0 +1,2 @@ +packages: + - anndata~=0.11.1 diff --git a/src/base/requirements/anndata_mudata.yaml b/src/base/requirements/anndata_mudata.yaml new file mode 100644 index 0000000..577b7e9 --- /dev/null +++ b/src/base/requirements/anndata_mudata.yaml @@ -0,0 +1,5 @@ +__merge__: [/src/base/requirements/anndata.yaml, .] +packages: + - mudata~=0.3.1 +script: | + exec("try:\n import awkward\nexcept ModuleNotFoundError:\n exit(0)\nelse: exit(1)") diff --git a/src/base/requirements/openpipeline_testutils.yaml b/src/base/requirements/openpipeline_testutils.yaml new file mode 100644 index 0000000..ae65ae6 --- /dev/null +++ b/src/base/requirements/openpipeline_testutils.yaml @@ -0,0 +1,2 @@ +github: + - openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils diff --git a/src/base/requirements/python_test_setup.yaml b/src/base/requirements/python_test_setup.yaml new file mode 100644 index 0000000..45552f2 --- /dev/null +++ b/src/base/requirements/python_test_setup.yaml @@ -0,0 +1,8 @@ +test_setup: + - type: apt + packages: + - git + - type: python + __merge__: + - /src/base/requirements/viashpy.yaml + - /src/base/requirements/openpipeline_testutils.yaml diff --git a/src/base/requirements/scanpy.yaml b/src/base/requirements/scanpy.yaml new file mode 100644 index 0000000..5c1af07 --- /dev/null +++ b/src/base/requirements/scanpy.yaml @@ -0,0 +1,2 @@ +packages: + - scanpy~=1.10.4 diff --git a/src/base/requirements/spatialdata-io.yaml b/src/base/requirements/spatialdata-io.yaml new file mode 100644 index 0000000..b7568e9 --- /dev/null +++ b/src/base/requirements/spatialdata-io.yaml @@ -0,0 +1,3 @@ +__merge__: [/src/base/requirements/spatialdata.yaml, .] +packages: + - spatialdata-io~=0.2.0 diff --git a/src/base/requirements/spatialdata.yaml b/src/base/requirements/spatialdata.yaml new file mode 100644 index 0000000..2a0379a --- /dev/null +++ b/src/base/requirements/spatialdata.yaml @@ -0,0 +1,2 @@ +packages: + - spatialdata~=0.4.1rc diff --git a/src/base/requirements/squidpy.yaml b/src/base/requirements/squidpy.yaml new file mode 100644 index 0000000..3d27832 --- /dev/null +++ b/src/base/requirements/squidpy.yaml @@ -0,0 +1,3 @@ +__merge__: [/src/base/requirements/spatialdata.yaml, .] +packages: + - squidpy~=1.6.5 diff --git a/src/base/requirements/viashpy.yaml b/src/base/requirements/viashpy.yaml new file mode 100644 index 0000000..64b6c2a --- /dev/null +++ b/src/base/requirements/viashpy.yaml @@ -0,0 +1,2 @@ +packages: + - viashpy==0.9.0 diff --git a/src/convert/from_cosmx_to_h5mu/config.vsh.yaml b/src/convert/from_cosmx_to_h5mu/config.vsh.yaml index 83e75d4..cf88726 100644 --- a/src/convert/from_cosmx_to_h5mu/config.vsh.yaml +++ b/src/convert/from_cosmx_to_h5mu/config.vsh.yaml @@ -52,17 +52,8 @@ engines: packages: - procps - type: python - packages: - - squidpy~=1.6.5 - - mudata~=0.3.1 - test_setup: - - type: apt - packages: - - git - - type: python - packages: - - viashpy==0.8.0 - github: openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils + __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/squidpy.yaml] + __merge__: [ /src/base/requirements/python_test_setup.yaml, .] runners: - type: executable - type: nextflow diff --git a/src/convert/from_cosmx_to_spatialexperiment/script.R b/src/convert/from_cosmx_to_spatialexperiment/script.R index e332a13..e6734e1 100644 --- a/src/convert/from_cosmx_to_spatialexperiment/script.R +++ b/src/convert/from_cosmx_to_spatialexperiment/script.R @@ -6,12 +6,14 @@ par <- list( add_tx_path = TRUE, add_polygon_path = FALSE, add_fov_positions = TRUE, - alternative_experiment_features = c("NegPrb", "Negative", "SystemControl", "FalseCode"), + alternative_experiment_features = c( + "NegPrb", "Negative", "SystemControl", "FalseCode" + ), output = "spe_cosmx_test.rds" ) ### VIASH END -if (par$add_polygon_path == FALSE & par$add_tx_path == FALSE) { +if (par$add_polygon_path == FALSE && par$add_tx_path == FALSE) { add_parquet_paths <- FALSE } else { add_parquet_paths <- TRUE diff --git a/src/convert/from_cosmx_to_spatialexperiment/test.R b/src/convert/from_cosmx_to_spatialexperiment/test.R index d6c517e..bbdd5b3 100644 --- a/src/convert/from_cosmx_to_spatialexperiment/test.R +++ b/src/convert/from_cosmx_to_spatialexperiment/test.R @@ -4,7 +4,7 @@ library(SpatialExperiment) ## VIASH START meta <- list( - executable = "target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment", + executable = "./from_cosmx_to_spatialexperiment", resources_dir = "resources_test/cosmx/", name = "from_cosmx_to_spatialexperiment" ) @@ -42,7 +42,10 @@ expect_is(obj, "SpatialExperiment") # Assay structure expect_equal(names(slot(obj, "assays")), "counts") # Spatial coordinates -expect_equal(spatialCoordsNames(obj), c("CenterX_global_px", "CenterY_global_px")) +expect_equal( + spatialCoordsNames(obj), + c("CenterX_global_px", "CenterY_global_px") +) # Alternative experiments expect_equal(altExpNames(obj), c("NegPrb")) # Metadata components @@ -96,7 +99,10 @@ expect_is(obj_ext, "SpatialExperiment") # Assay structure expect_equal(names(slot(obj_ext, "assays")), "counts") # Spatial coordinates -expect_equal(spatialCoordsNames(obj_ext), c("CenterX_global_px", "CenterY_global_px")) +expect_equal( + spatialCoordsNames(obj_ext), + c("CenterX_global_px", "CenterY_global_px") +) # Alternative experiments expect_length(altExpNames(obj_ext), 0) # Metadata components diff --git a/src/convert/from_spatialdata_to_h5mu/config.vsh.yaml b/src/convert/from_spatialdata_to_h5mu/config.vsh.yaml index 68e86d7..b1ee832 100644 --- a/src/convert/from_spatialdata_to_h5mu/config.vsh.yaml +++ b/src/convert/from_spatialdata_to_h5mu/config.vsh.yaml @@ -46,18 +46,8 @@ engines: packages: - procps - type: python - packages: - - spatialdata~=0.4.0 - - spatialdata-io~=0.2.0 - - mudata~=0.3.1 - test_setup: - - type: apt - packages: - - git - - type: python - packages: - - viashpy==0.8.0 - github: openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils + __merge__: [/src/base/requirements/anndata_mudata.yaml, /src/base/requirements/spatialdata.yaml] + __merge__: [ /src/base/requirements/python_test_setup.yaml, .] runners: - type: executable - type: nextflow diff --git a/src/convert/from_xenium_to_spatialdata/config.vsh.yaml b/src/convert/from_xenium_to_spatialdata/config.vsh.yaml index b468d86..9160bec 100644 --- a/src/convert/from_xenium_to_spatialdata/config.vsh.yaml +++ b/src/convert/from_xenium_to_spatialdata/config.vsh.yaml @@ -90,17 +90,8 @@ engines: packages: - procps - type: python - packages: - - spatialdata-io~=0.1.7 - test_setup: - - type: apt - packages: - - git - - type: python - packages: - - viashpy==0.8.0 - - spatialdata~=0.3.0 - github: openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils + __merge__: [ /src/base/requirements/spatialdata-io.yaml ] + __merge__: [ /src/base/requirements/python_test_setup.yaml, .] runners: - type: executable - type: nextflow diff --git a/src/convert/from_xenium_to_spatialexperiment/script.R b/src/convert/from_xenium_to_spatialexperiment/script.R index c60abb0..4060410 100644 --- a/src/convert/from_xenium_to_spatialexperiment/script.R +++ b/src/convert/from_xenium_to_spatialexperiment/script.R @@ -5,7 +5,10 @@ par <- list( input = "resources_test/xenium/xenium_tiny", add_experiment_xenium = TRUE, add_parquet_paths = TRUE, - alternative_experiment_features = c("NegControlProbe", "UnassignedCodeword", "NegControlCodeword", "antisense", "BLANK"), + alternative_experiment_features = c( + "NegControlProbe", "UnassignedCodeword", + "NegControlCodeword", "antisense", "BLANK" + ), output = "spe_test.rds" ) ### VIASH END diff --git a/src/convert/from_xenium_to_spatialexperiment/test.R b/src/convert/from_xenium_to_spatialexperiment/test.R index 0e8077d..22f1095 100644 --- a/src/convert/from_xenium_to_spatialexperiment/test.R +++ b/src/convert/from_xenium_to_spatialexperiment/test.R @@ -4,7 +4,7 @@ library(SpatialExperiment) ## VIASH START meta <- list( - executable = "target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment", + executable = "./from_xenium_to_spatialexperiment", resources_dir = "resources_test/xenium", name = "from_xenium_to_spatial_experiment" ) @@ -42,9 +42,14 @@ expect_equal(names(slot(obj, "assays")), "counts") # Spatial coordinates expect_equal(spatialCoordsNames(obj), c("x_centroid", "y_centroid")) # Alternative experiments -expect_equal(altExpNames(obj), c("NegControlProbe", "UnassignedCodeword", "NegControlCodeword")) +expect_equal( + altExpNames(obj), + c("NegControlProbe", "UnassignedCodeword", "NegControlCodeword") +) # Metadata components -metadata_components <- c("experiment.xenium", "transcripts", "cell_boundaries", "nucleus_boundaries") +metadata_components <- c( + "experiment.xenium", "transcripts", "cell_boundaries", "nucleus_boundaries" +) expect_named( metadata(obj), metadata_components, diff --git a/src/filter/subset_cosmx/config.vsh.yaml b/src/filter/subset_cosmx/config.vsh.yaml index ae08909..df9a068 100644 --- a/src/filter/subset_cosmx/config.vsh.yaml +++ b/src/filter/subset_cosmx/config.vsh.yaml @@ -62,16 +62,8 @@ engines: packages: - procps - type: python - packages: - - squidpy~=1.6.5 - test_setup: - - type: apt - packages: - - git - - type: python - packages: - - viashpy==0.8.0 - github: openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils + __merge__: [ /src/base/requirements/squidpy.yaml ] + __merge__: [ /src/base/requirements/python_test_setup.yaml, .] runners: - type: executable - type: nextflow diff --git a/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml index b8fec8a..cc064f9 100644 --- a/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml +++ b/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml @@ -198,8 +198,13 @@ engines: - type: "python" user: false packages: - - "squidpy~=1.6.5" + - "anndata~=0.11.1" - "mudata~=0.3.1" + - "spatialdata~=0.4.1rc" + - "squidpy~=1.6.5" + script: + - "exec(\"try:\\n import awkward\\nexcept ModuleNotFoundError:\\n exit(0)\\\ + nelse: exit(1)\")" upgrade: true test_setup: - type: "apt" @@ -209,7 +214,7 @@ engines: - type: "python" user: false packages: - - "viashpy==0.8.0" + - "viashpy==0.9.0" github: - "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils" upgrade: true @@ -224,7 +229,7 @@ build_info: output: "target/executable/convert/from_cosmx_to_h5mu" executable: "target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu" viash_version: "0.9.4" - git_commit: "280b21fc21238c6e7b2e76089deffdef5d979b34" + git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu b/target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu index e400419..612532b 100755 --- a/target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu +++ b/target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu @@ -454,13 +454,14 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* RUN pip install --upgrade pip && \ - pip install --upgrade --no-cache-dir "squidpy~=1.6.5" "mudata~=0.3.1" + pip install --upgrade --no-cache-dir "anndata~=0.11.1" "mudata~=0.3.1" "spatialdata~=0.4.1rc" "squidpy~=1.6.5" && \ + python -c 'exec("try:\n import awkward\nexcept ModuleNotFoundError:\n exit(0)\nelse: exit(1)")' LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component convert from_cosmx_to_h5mu" -LABEL org.opencontainers.image.created="2025-07-24T15:22:52Z" +LABEL org.opencontainers.image.created="2025-08-18T07:54:17Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="280b21fc21238c6e7b2e76089deffdef5d979b34" +LABEL org.opencontainers.image.revision="226d7de695d56f116dd1ba8e08a51ebf63b153b3" LABEL org.opencontainers.image.version="build_main" VIASHDOCKER diff --git a/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml b/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml index 0e595f5..eefe808 100644 --- a/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml +++ b/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml @@ -236,7 +236,7 @@ build_info: output: "target/executable/convert/from_cosmx_to_spatialexperiment" executable: "target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment" viash_version: "0.9.4" - git_commit: "280b21fc21238c6e7b2e76089deffdef5d979b34" + git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment b/target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment index 5cbed1d..26f6315 100755 --- a/target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment +++ b/target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment @@ -457,9 +457,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("BiocManager", quietly LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component convert from_cosmx_to_spatialexperiment" -LABEL org.opencontainers.image.created="2025-07-24T15:22:53Z" +LABEL org.opencontainers.image.created="2025-08-18T07:54:16Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="280b21fc21238c6e7b2e76089deffdef5d979b34" +LABEL org.opencontainers.image.revision="226d7de695d56f116dd1ba8e08a51ebf63b153b3" LABEL org.opencontainers.image.version="build_main" VIASHDOCKER @@ -1221,7 +1221,7 @@ rm(.viash_orig_warn) ### VIASH END -if (par\$add_polygon_path == FALSE & par\$add_tx_path == FALSE) { +if (par\$add_polygon_path == FALSE && par\$add_tx_path == FALSE) { add_parquet_paths <- FALSE } else { add_parquet_paths <- TRUE diff --git a/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml index a6bed1d..0507bbe 100644 --- a/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml +++ b/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml @@ -194,9 +194,12 @@ engines: - type: "python" user: false packages: - - "spatialdata~=0.4.0" - - "spatialdata-io~=0.2.0" + - "anndata~=0.11.1" - "mudata~=0.3.1" + - "spatialdata~=0.4.1rc" + script: + - "exec(\"try:\\n import awkward\\nexcept ModuleNotFoundError:\\n exit(0)\\\ + nelse: exit(1)\")" upgrade: true test_setup: - type: "apt" @@ -206,7 +209,7 @@ engines: - type: "python" user: false packages: - - "viashpy==0.8.0" + - "viashpy==0.9.0" github: - "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils" upgrade: true @@ -221,7 +224,7 @@ build_info: output: "target/executable/convert/from_spatialdata_to_h5mu" executable: "target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu" viash_version: "0.9.4" - git_commit: "280b21fc21238c6e7b2e76089deffdef5d979b34" + git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu b/target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu index fd17b4f..b1e1b1e 100755 --- a/target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu +++ b/target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu @@ -454,13 +454,14 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* RUN pip install --upgrade pip && \ - pip install --upgrade --no-cache-dir "spatialdata~=0.4.0" "spatialdata-io~=0.2.0" "mudata~=0.3.1" + pip install --upgrade --no-cache-dir "anndata~=0.11.1" "mudata~=0.3.1" "spatialdata~=0.4.1rc" && \ + python -c 'exec("try:\n import awkward\nexcept ModuleNotFoundError:\n exit(0)\nelse: exit(1)")' LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component convert from_spatialdata_to_h5mu" -LABEL org.opencontainers.image.created="2025-07-24T15:22:52Z" +LABEL org.opencontainers.image.created="2025-08-18T07:54:16Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="280b21fc21238c6e7b2e76089deffdef5d979b34" +LABEL org.opencontainers.image.revision="226d7de695d56f116dd1ba8e08a51ebf63b153b3" LABEL org.opencontainers.image.version="build_main" VIASHDOCKER diff --git a/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml b/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml index e7da35e..7061c22 100644 --- a/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml +++ b/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml @@ -292,7 +292,8 @@ engines: - type: "python" user: false packages: - - "spatialdata-io~=0.1.7" + - "spatialdata~=0.4.1rc" + - "spatialdata-io~=0.2.0" upgrade: true test_setup: - type: "apt" @@ -302,8 +303,7 @@ engines: - type: "python" user: false packages: - - "viashpy==0.8.0" - - "spatialdata~=0.3.0" + - "viashpy==0.9.0" github: - "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils" upgrade: true @@ -318,7 +318,7 @@ build_info: output: "target/executable/convert/from_xenium_to_spatialdata" executable: "target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata" viash_version: "0.9.4" - git_commit: "280b21fc21238c6e7b2e76089deffdef5d979b34" + git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata b/target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata index 7d37d1b..de045b2 100755 --- a/target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata +++ b/target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata @@ -454,13 +454,13 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* RUN pip install --upgrade pip && \ - pip install --upgrade --no-cache-dir "spatialdata-io~=0.1.7" + pip install --upgrade --no-cache-dir "spatialdata~=0.4.1rc" "spatialdata-io~=0.2.0" LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component convert from_xenium_to_spatialdata" -LABEL org.opencontainers.image.created="2025-07-24T15:22:52Z" +LABEL org.opencontainers.image.created="2025-08-18T07:54:17Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="280b21fc21238c6e7b2e76089deffdef5d979b34" +LABEL org.opencontainers.image.revision="226d7de695d56f116dd1ba8e08a51ebf63b153b3" LABEL org.opencontainers.image.version="build_main" VIASHDOCKER diff --git a/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml b/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml index 6168596..2b96ebc 100644 --- a/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml +++ b/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml @@ -226,7 +226,7 @@ build_info: output: "target/executable/convert/from_xenium_to_spatialexperiment" executable: "target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment" viash_version: "0.9.4" - git_commit: "280b21fc21238c6e7b2e76089deffdef5d979b34" + git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment b/target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment index 6bcefba..9fec37a 100755 --- a/target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment +++ b/target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment @@ -457,9 +457,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("BiocManager", quietly LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component convert from_xenium_to_spatialexperiment" -LABEL org.opencontainers.image.created="2025-07-24T15:22:53Z" +LABEL org.opencontainers.image.created="2025-08-18T07:54:16Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="280b21fc21238c6e7b2e76089deffdef5d979b34" +LABEL org.opencontainers.image.revision="226d7de695d56f116dd1ba8e08a51ebf63b153b3" LABEL org.opencontainers.image.version="build_main" VIASHDOCKER diff --git a/target/executable/filter/subset_cosmx/.config.vsh.yaml b/target/executable/filter/subset_cosmx/.config.vsh.yaml index f2e860a..4a265a6 100644 --- a/target/executable/filter/subset_cosmx/.config.vsh.yaml +++ b/target/executable/filter/subset_cosmx/.config.vsh.yaml @@ -205,6 +205,7 @@ engines: - type: "python" user: false packages: + - "spatialdata~=0.4.1rc" - "squidpy~=1.6.5" upgrade: true test_setup: @@ -215,7 +216,7 @@ engines: - type: "python" user: false packages: - - "viashpy==0.8.0" + - "viashpy==0.9.0" github: - "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils" upgrade: true @@ -230,7 +231,7 @@ build_info: output: "target/executable/filter/subset_cosmx" executable: "target/executable/filter/subset_cosmx/subset_cosmx" viash_version: "0.9.4" - git_commit: "280b21fc21238c6e7b2e76089deffdef5d979b34" + git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/executable/filter/subset_cosmx/subset_cosmx b/target/executable/filter/subset_cosmx/subset_cosmx index 2362e05..2bf52d6 100755 --- a/target/executable/filter/subset_cosmx/subset_cosmx +++ b/target/executable/filter/subset_cosmx/subset_cosmx @@ -454,13 +454,13 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* RUN pip install --upgrade pip && \ - pip install --upgrade --no-cache-dir "squidpy~=1.6.5" + pip install --upgrade --no-cache-dir "spatialdata~=0.4.1rc" "squidpy~=1.6.5" LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component filter subset_cosmx" -LABEL org.opencontainers.image.created="2025-07-24T15:22:52Z" +LABEL org.opencontainers.image.created="2025-08-18T07:54:16Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="280b21fc21238c6e7b2e76089deffdef5d979b34" +LABEL org.opencontainers.image.revision="226d7de695d56f116dd1ba8e08a51ebf63b153b3" LABEL org.opencontainers.image.version="build_main" VIASHDOCKER diff --git a/target/executable/mapping/spaceranger_count/.config.vsh.yaml b/target/executable/mapping/spaceranger_count/.config.vsh.yaml index b20f2db..36c86df 100644 --- a/target/executable/mapping/spaceranger_count/.config.vsh.yaml +++ b/target/executable/mapping/spaceranger_count/.config.vsh.yaml @@ -430,7 +430,7 @@ build_info: output: "target/executable/mapping/spaceranger_count" executable: "target/executable/mapping/spaceranger_count/spaceranger_count" viash_version: "0.9.4" - git_commit: "280b21fc21238c6e7b2e76089deffdef5d979b34" + git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/executable/mapping/spaceranger_count/spaceranger_count b/target/executable/mapping/spaceranger_count/spaceranger_count index ebe5ef9..34e392f 100755 --- a/target/executable/mapping/spaceranger_count/spaceranger_count +++ b/target/executable/mapping/spaceranger_count/spaceranger_count @@ -453,9 +453,9 @@ apt upgrade -y && apt install -y procps && rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.authors="Jakub Majercik" LABEL org.opencontainers.image.description="Companion container for running component mapping spaceranger_count" -LABEL org.opencontainers.image.created="2025-07-24T15:22:52Z" +LABEL org.opencontainers.image.created="2025-08-18T07:54:17Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="280b21fc21238c6e7b2e76089deffdef5d979b34" +LABEL org.opencontainers.image.revision="226d7de695d56f116dd1ba8e08a51ebf63b153b3" LABEL org.opencontainers.image.version="build_main" VIASHDOCKER diff --git a/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml index dbe0def..10a5ba6 100644 --- a/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml @@ -198,8 +198,13 @@ engines: - type: "python" user: false packages: - - "squidpy~=1.6.5" + - "anndata~=0.11.1" - "mudata~=0.3.1" + - "spatialdata~=0.4.1rc" + - "squidpy~=1.6.5" + script: + - "exec(\"try:\\n import awkward\\nexcept ModuleNotFoundError:\\n exit(0)\\\ + nelse: exit(1)\")" upgrade: true test_setup: - type: "apt" @@ -209,7 +214,7 @@ engines: - type: "python" user: false packages: - - "viashpy==0.8.0" + - "viashpy==0.9.0" github: - "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils" upgrade: true @@ -224,7 +229,7 @@ build_info: output: "target/nextflow/convert/from_cosmx_to_h5mu" executable: "target/nextflow/convert/from_cosmx_to_h5mu/main.nf" viash_version: "0.9.4" - git_commit: "280b21fc21238c6e7b2e76089deffdef5d979b34" + git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/nextflow/convert/from_cosmx_to_h5mu/main.nf b/target/nextflow/convert/from_cosmx_to_h5mu/main.nf index 90c9a85..5a732aa 100644 --- a/target/nextflow/convert/from_cosmx_to_h5mu/main.nf +++ b/target/nextflow/convert/from_cosmx_to_h5mu/main.nf @@ -3294,8 +3294,13 @@ meta = [ "type" : "python", "user" : false, "packages" : [ - "squidpy~=1.6.5", - "mudata~=0.3.1" + "anndata~=0.11.1", + "mudata~=0.3.1", + "spatialdata~=0.4.1rc", + "squidpy~=1.6.5" + ], + "script" : [ + "exec(\\"try:\\\\n import awkward\\\\nexcept ModuleNotFoundError:\\\\n exit(0)\\\\nelse: exit(1)\\")" ], "upgrade" : true } @@ -3312,7 +3317,7 @@ meta = [ "type" : "python", "user" : false, "packages" : [ - "viashpy==0.8.0" + "viashpy==0.9.0" ], "github" : [ "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils" @@ -3332,7 +3337,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_h5mu", "viash_version" : "0.9.4", - "git_commit" : "280b21fc21238c6e7b2e76089deffdef5d979b34", + "git_commit" : "226d7de695d56f116dd1ba8e08a51ebf63b153b3", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { diff --git a/target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml b/target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml index 61aa4d6..3a6b0a9 100644 --- a/target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml +++ b/target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml @@ -236,7 +236,7 @@ build_info: output: "target/nextflow/convert/from_cosmx_to_spatialexperiment" executable: "target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf" viash_version: "0.9.4" - git_commit: "280b21fc21238c6e7b2e76089deffdef5d979b34" + git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf b/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf index cc52a55..cf9dd51 100644 --- a/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf +++ b/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf @@ -3328,7 +3328,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_spatialexperiment", "viash_version" : "0.9.4", - "git_commit" : "280b21fc21238c6e7b2e76089deffdef5d979b34", + "git_commit" : "226d7de695d56f116dd1ba8e08a51ebf63b153b3", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3430,7 +3430,7 @@ rm(.viash_orig_warn) ### VIASH END -if (par\\$add_polygon_path == FALSE & par\\$add_tx_path == FALSE) { +if (par\\$add_polygon_path == FALSE && par\\$add_tx_path == FALSE) { add_parquet_paths <- FALSE } else { add_parquet_paths <- TRUE diff --git a/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml index d7a8d04..5bac860 100644 --- a/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml @@ -194,9 +194,12 @@ engines: - type: "python" user: false packages: - - "spatialdata~=0.4.0" - - "spatialdata-io~=0.2.0" + - "anndata~=0.11.1" - "mudata~=0.3.1" + - "spatialdata~=0.4.1rc" + script: + - "exec(\"try:\\n import awkward\\nexcept ModuleNotFoundError:\\n exit(0)\\\ + nelse: exit(1)\")" upgrade: true test_setup: - type: "apt" @@ -206,7 +209,7 @@ engines: - type: "python" user: false packages: - - "viashpy==0.8.0" + - "viashpy==0.9.0" github: - "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils" upgrade: true @@ -221,7 +224,7 @@ build_info: output: "target/nextflow/convert/from_spatialdata_to_h5mu" executable: "target/nextflow/convert/from_spatialdata_to_h5mu/main.nf" viash_version: "0.9.4" - git_commit: "280b21fc21238c6e7b2e76089deffdef5d979b34" + git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf b/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf index b9a8b21..c021255 100644 --- a/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf +++ b/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf @@ -3294,9 +3294,12 @@ meta = [ "type" : "python", "user" : false, "packages" : [ - "spatialdata~=0.4.0", - "spatialdata-io~=0.2.0", - "mudata~=0.3.1" + "anndata~=0.11.1", + "mudata~=0.3.1", + "spatialdata~=0.4.1rc" + ], + "script" : [ + "exec(\\"try:\\\\n import awkward\\\\nexcept ModuleNotFoundError:\\\\n exit(0)\\\\nelse: exit(1)\\")" ], "upgrade" : true } @@ -3313,7 +3316,7 @@ meta = [ "type" : "python", "user" : false, "packages" : [ - "viashpy==0.8.0" + "viashpy==0.9.0" ], "github" : [ "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils" @@ -3333,7 +3336,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_spatialdata_to_h5mu", "viash_version" : "0.9.4", - "git_commit" : "280b21fc21238c6e7b2e76089deffdef5d979b34", + "git_commit" : "226d7de695d56f116dd1ba8e08a51ebf63b153b3", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { diff --git a/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml b/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml index 2304ce7..0e8c690 100644 --- a/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml +++ b/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml @@ -292,7 +292,8 @@ engines: - type: "python" user: false packages: - - "spatialdata-io~=0.1.7" + - "spatialdata~=0.4.1rc" + - "spatialdata-io~=0.2.0" upgrade: true test_setup: - type: "apt" @@ -302,8 +303,7 @@ engines: - type: "python" user: false packages: - - "viashpy==0.8.0" - - "spatialdata~=0.3.0" + - "viashpy==0.9.0" github: - "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils" upgrade: true @@ -318,7 +318,7 @@ build_info: output: "target/nextflow/convert/from_xenium_to_spatialdata" executable: "target/nextflow/convert/from_xenium_to_spatialdata/main.nf" viash_version: "0.9.4" - git_commit: "280b21fc21238c6e7b2e76089deffdef5d979b34" + git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/nextflow/convert/from_xenium_to_spatialdata/main.nf b/target/nextflow/convert/from_xenium_to_spatialdata/main.nf index 05b3505..ca880f0 100644 --- a/target/nextflow/convert/from_xenium_to_spatialdata/main.nf +++ b/target/nextflow/convert/from_xenium_to_spatialdata/main.nf @@ -3393,7 +3393,8 @@ meta = [ "type" : "python", "user" : false, "packages" : [ - "spatialdata-io~=0.1.7" + "spatialdata~=0.4.1rc", + "spatialdata-io~=0.2.0" ], "upgrade" : true } @@ -3410,8 +3411,7 @@ meta = [ "type" : "python", "user" : false, "packages" : [ - "viashpy==0.8.0", - "spatialdata~=0.3.0" + "viashpy==0.9.0" ], "github" : [ "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils" @@ -3431,7 +3431,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialdata", "viash_version" : "0.9.4", - "git_commit" : "280b21fc21238c6e7b2e76089deffdef5d979b34", + "git_commit" : "226d7de695d56f116dd1ba8e08a51ebf63b153b3", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { diff --git a/target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml b/target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml index 53ec675..d99d398 100644 --- a/target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml +++ b/target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml @@ -226,7 +226,7 @@ build_info: output: "target/nextflow/convert/from_xenium_to_spatialexperiment" executable: "target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf" viash_version: "0.9.4" - git_commit: "280b21fc21238c6e7b2e76089deffdef5d979b34" + git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf b/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf index 1ed601b..4123699 100644 --- a/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf +++ b/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf @@ -3317,7 +3317,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialexperiment", "viash_version" : "0.9.4", - "git_commit" : "280b21fc21238c6e7b2e76089deffdef5d979b34", + "git_commit" : "226d7de695d56f116dd1ba8e08a51ebf63b153b3", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { diff --git a/target/nextflow/filter/subset_cosmx/.config.vsh.yaml b/target/nextflow/filter/subset_cosmx/.config.vsh.yaml index 8ea68df..e53ec85 100644 --- a/target/nextflow/filter/subset_cosmx/.config.vsh.yaml +++ b/target/nextflow/filter/subset_cosmx/.config.vsh.yaml @@ -205,6 +205,7 @@ engines: - type: "python" user: false packages: + - "spatialdata~=0.4.1rc" - "squidpy~=1.6.5" upgrade: true test_setup: @@ -215,7 +216,7 @@ engines: - type: "python" user: false packages: - - "viashpy==0.8.0" + - "viashpy==0.9.0" github: - "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils" upgrade: true @@ -230,7 +231,7 @@ build_info: output: "target/nextflow/filter/subset_cosmx" executable: "target/nextflow/filter/subset_cosmx/main.nf" viash_version: "0.9.4" - git_commit: "280b21fc21238c6e7b2e76089deffdef5d979b34" + git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/nextflow/filter/subset_cosmx/main.nf b/target/nextflow/filter/subset_cosmx/main.nf index fb46aef..38ee5c0 100644 --- a/target/nextflow/filter/subset_cosmx/main.nf +++ b/target/nextflow/filter/subset_cosmx/main.nf @@ -3301,6 +3301,7 @@ meta = [ "type" : "python", "user" : false, "packages" : [ + "spatialdata~=0.4.1rc", "squidpy~=1.6.5" ], "upgrade" : true @@ -3318,7 +3319,7 @@ meta = [ "type" : "python", "user" : false, "packages" : [ - "viashpy==0.8.0" + "viashpy==0.9.0" ], "github" : [ "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils" @@ -3338,7 +3339,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/filter/subset_cosmx", "viash_version" : "0.9.4", - "git_commit" : "280b21fc21238c6e7b2e76089deffdef5d979b34", + "git_commit" : "226d7de695d56f116dd1ba8e08a51ebf63b153b3", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { diff --git a/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml b/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml index 4b8d951..6e557fd 100644 --- a/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml +++ b/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml @@ -430,7 +430,7 @@ build_info: output: "target/nextflow/mapping/spaceranger_count" executable: "target/nextflow/mapping/spaceranger_count/main.nf" viash_version: "0.9.4" - git_commit: "280b21fc21238c6e7b2e76089deffdef5d979b34" + git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" diff --git a/target/nextflow/mapping/spaceranger_count/main.nf b/target/nextflow/mapping/spaceranger_count/main.nf index 5666935..cb81e78 100644 --- a/target/nextflow/mapping/spaceranger_count/main.nf +++ b/target/nextflow/mapping/spaceranger_count/main.nf @@ -3554,7 +3554,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/mapping/spaceranger_count", "viash_version" : "0.9.4", - "git_commit" : "280b21fc21238c6e7b2e76089deffdef5d979b34", + "git_commit" : "226d7de695d56f116dd1ba8e08a51ebf63b153b3", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { diff --git a/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml b/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml index 7453c51..d631187 100644 --- a/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml +++ b/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml @@ -648,7 +648,7 @@ build_info: output: "target/nextflow/workflows/multiomics/spatial_process_samples" executable: "target/nextflow/workflows/multiomics/spatial_process_samples/main.nf" viash_version: "0.9.4" - git_commit: "280b21fc21238c6e7b2e76089deffdef5d979b34" + git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" dependencies: - "target/dependencies/github/openpipelines-bio/openpipeline/disable-scrublet_build/nextflow/workflows/multiomics/process_samples" diff --git a/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf b/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf index c15ef59..5baa50a 100644 --- a/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf +++ b/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf @@ -3819,7 +3819,7 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/multiomics/spatial_process_samples", "viash_version" : "0.9.4", - "git_commit" : "280b21fc21238c6e7b2e76089deffdef5d979b34", + "git_commit" : "226d7de695d56f116dd1ba8e08a51ebf63b153b3", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { diff --git a/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml b/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml index b138ebd..23fcbfc 100644 --- a/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml +++ b/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml @@ -391,7 +391,7 @@ build_info: output: "target/nextflow/workflows/qc/spatial_qc" executable: "target/nextflow/workflows/qc/spatial_qc/main.nf" viash_version: "0.9.4" - git_commit: "280b21fc21238c6e7b2e76089deffdef5d979b34" + git_commit: "226d7de695d56f116dd1ba8e08a51ebf63b153b3" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" dependencies: - "target/dependencies/github/openpipelines-bio/openpipeline/2.1.2/nextflow/workflows/qc/qc" diff --git a/target/nextflow/workflows/qc/spatial_qc/main.nf b/target/nextflow/workflows/qc/spatial_qc/main.nf index d1f933b..2220976 100644 --- a/target/nextflow/workflows/qc/spatial_qc/main.nf +++ b/target/nextflow/workflows/qc/spatial_qc/main.nf @@ -3511,7 +3511,7 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/qc/spatial_qc", "viash_version" : "0.9.4", - "git_commit" : "280b21fc21238c6e7b2e76089deffdef5d979b34", + "git_commit" : "226d7de695d56f116dd1ba8e08a51ebf63b153b3", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : {