diff --git a/_viash.yaml b/_viash.yaml index cab05aa..f103cd8 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -11,10 +11,6 @@ repositories: repo: openpipelines-bio/openpipeline type: github tag: 2.1.2 - - name: openpipeline_incubator - repo: openpipeline_incubator - type: vsh - tag: build/main info: test_resources: - type: s3 diff --git a/target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml index 0d5434c..111f86c 100644 --- a/target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml +++ b/target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml @@ -178,10 +178,6 @@ repositories: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" -- type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -294,7 +290,7 @@ 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: "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" + git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -309,10 +305,6 @@ package_config: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" - - type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu b/target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu index 52cabe5..df0115f 100755 --- a/target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu +++ b/target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu @@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component convert from_cells2stats_to_h5mu" -LABEL org.opencontainers.image.created="2025-08-21T08:53:51Z" +LABEL org.opencontainers.image.created="2025-08-22T08:22:46Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" +LABEL org.opencontainers.image.revision="6f308e6a3cca52f1283fbba734a3cdc858e18e1b" LABEL org.opencontainers.image.version="build_main" VIASHDOCKER 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 528cba4..98cfee3 100644 --- a/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml +++ b/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml @@ -106,10 +106,6 @@ repositories: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" -- type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -229,7 +225,7 @@ 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: "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" + git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -244,10 +240,6 @@ package_config: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" - - type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" viash_version: "0.9.4" source: "src" target: "target" 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 27c14b2..6aef839 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 @@ -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_cosmx_to_h5mu" -LABEL org.opencontainers.image.created="2025-08-21T08:53:53Z" +LABEL org.opencontainers.image.created="2025-08-22T08:22:48Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" +LABEL org.opencontainers.image.revision="6f308e6a3cca52f1283fbba734a3cdc858e18e1b" 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 ed0fba2..3bd4365 100644 --- a/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml +++ b/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml @@ -124,10 +124,6 @@ repositories: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" -- type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -236,7 +232,7 @@ 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: "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" + git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -251,10 +247,6 @@ package_config: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" - - type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" viash_version: "0.9.4" source: "src" target: "target" 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 29479d3..5c53f8e 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="2025-08-21T08:53:52Z" +LABEL org.opencontainers.image.created="2025-08-22T08:22:47Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" +LABEL org.opencontainers.image.revision="6f308e6a3cca52f1283fbba734a3cdc858e18e1b" LABEL org.opencontainers.image.version="build_main" VIASHDOCKER 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 7e4ee59..ee5d6d0 100644 --- a/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml +++ b/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml @@ -102,10 +102,6 @@ repositories: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" -- type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -224,7 +220,7 @@ 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: "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" + git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -239,10 +235,6 @@ package_config: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" - - type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" viash_version: "0.9.4" source: "src" target: "target" 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 4b4a8eb..1312c70 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 @@ -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="2025-08-21T08:53:52Z" +LABEL org.opencontainers.image.created="2025-08-22T08:22:47Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" +LABEL org.opencontainers.image.revision="6f308e6a3cca52f1283fbba734a3cdc858e18e1b" LABEL org.opencontainers.image.version="build_main" VIASHDOCKER diff --git a/target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml index 13bb5d4..f806f1c 100644 --- a/target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml +++ b/target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml @@ -120,10 +120,6 @@ repositories: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" -- type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -237,7 +233,7 @@ 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: "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" + git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -252,10 +248,6 @@ package_config: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" - - type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu b/target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu index fbf896b..fc84cca 100755 --- a/target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu +++ b/target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu @@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component convert from_xenium_to_h5mu" -LABEL org.opencontainers.image.created="2025-08-21T08:53:52Z" +LABEL org.opencontainers.image.created="2025-08-22T08:22:47Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" +LABEL org.opencontainers.image.revision="6f308e6a3cca52f1283fbba734a3cdc858e18e1b" 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 a042ba8..447b8f0 100644 --- a/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml +++ b/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml @@ -200,10 +200,6 @@ repositories: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" -- type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -318,7 +314,7 @@ 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: "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" + git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -333,10 +329,6 @@ package_config: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" - - type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" viash_version: "0.9.4" source: "src" target: "target" 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 bb0c4b2..5e1667a 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 @@ -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 convert from_xenium_to_spatialdata" -LABEL org.opencontainers.image.created="2025-08-21T08:53:52Z" +LABEL org.opencontainers.image.created="2025-08-22T08:22:47Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" +LABEL org.opencontainers.image.revision="6f308e6a3cca52f1283fbba734a3cdc858e18e1b" 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 6b09765..483d6ef 100644 --- a/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml +++ b/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml @@ -114,10 +114,6 @@ repositories: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" -- type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -226,7 +222,7 @@ 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: "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" + git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -241,10 +237,6 @@ package_config: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" - - type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" viash_version: "0.9.4" source: "src" target: "target" 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 aeb938f..4d639e1 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="2025-08-21T08:53:52Z" +LABEL org.opencontainers.image.created="2025-08-22T08:22:47Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" +LABEL org.opencontainers.image.revision="6f308e6a3cca52f1283fbba734a3cdc858e18e1b" 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 9b9bbb6..f5badef 100644 --- a/target/executable/filter/subset_cosmx/.config.vsh.yaml +++ b/target/executable/filter/subset_cosmx/.config.vsh.yaml @@ -113,10 +113,6 @@ repositories: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" -- type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -231,7 +227,7 @@ build_info: output: "target/executable/filter/subset_cosmx" executable: "target/executable/filter/subset_cosmx/subset_cosmx" viash_version: "0.9.4" - git_commit: "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" + git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -246,10 +242,6 @@ package_config: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" - - type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/executable/filter/subset_cosmx/subset_cosmx b/target/executable/filter/subset_cosmx/subset_cosmx index da10c06..db0f380 100755 --- a/target/executable/filter/subset_cosmx/subset_cosmx +++ b/target/executable/filter/subset_cosmx/subset_cosmx @@ -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="2025-08-21T08:53:51Z" +LABEL org.opencontainers.image.created="2025-08-22T08:22:46Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" +LABEL org.opencontainers.image.revision="6f308e6a3cca52f1283fbba734a3cdc858e18e1b" 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 ab281de..3613d33 100644 --- a/target/executable/mapping/spaceranger_count/.config.vsh.yaml +++ b/target/executable/mapping/spaceranger_count/.config.vsh.yaml @@ -330,10 +330,6 @@ repositories: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" -- type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" keywords: - "spaceranger" links: @@ -430,7 +426,7 @@ build_info: output: "target/executable/mapping/spaceranger_count" executable: "target/executable/mapping/spaceranger_count/spaceranger_count" viash_version: "0.9.4" - git_commit: "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" + git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -445,10 +441,6 @@ package_config: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" - - type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/executable/mapping/spaceranger_count/spaceranger_count b/target/executable/mapping/spaceranger_count/spaceranger_count index 03115c1..e640da3 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="2025-08-21T08:53:53Z" +LABEL org.opencontainers.image.created="2025-08-22T08:22:48Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" +LABEL org.opencontainers.image.revision="6f308e6a3cca52f1283fbba734a3cdc858e18e1b" LABEL org.opencontainers.image.version="build_main" VIASHDOCKER diff --git a/target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml index aef8d8b..e43b9a5 100644 --- a/target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml @@ -178,10 +178,6 @@ repositories: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" -- type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -294,7 +290,7 @@ 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: "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" + git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -309,10 +305,6 @@ package_config: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" - - type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/nextflow/convert/from_cells2stats_to_h5mu/main.nf b/target/nextflow/convert/from_cells2stats_to_h5mu/main.nf index 8f7c1be..a6523e3 100644 --- a/target/nextflow/convert/from_cells2stats_to_h5mu/main.nf +++ b/target/nextflow/convert/from_cells2stats_to_h5mu/main.nf @@ -3243,12 +3243,6 @@ meta = [ "name" : "openpipeline", "repo" : "openpipelines-bio/openpipeline", "tag" : "2.1.2" - }, - { - "type" : "vsh", - "name" : "openpipeline_incubator", - "repo" : "openpipeline_incubator", - "tag" : "build/main" } ], "links" : { @@ -3388,7 +3382,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_cells2stats_to_h5mu", "viash_version" : "0.9.4", - "git_commit" : "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8", + "git_commit" : "6f308e6a3cca52f1283fbba734a3cdc858e18e1b", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3409,12 +3403,6 @@ meta = [ "name" : "openpipeline", "repo" : "openpipelines-bio/openpipeline", "tag" : "2.1.2" - }, - { - "type" : "vsh", - "name" : "openpipeline_incubator", - "repo" : "openpipeline_incubator", - "tag" : "build/main" } ], "viash_version" : "0.9.4", 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 37e1e0a..aa45696 100644 --- a/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml @@ -106,10 +106,6 @@ repositories: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" -- type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -229,7 +225,7 @@ 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: "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" + git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -244,10 +240,6 @@ package_config: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" - - type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/nextflow/convert/from_cosmx_to_h5mu/main.nf b/target/nextflow/convert/from_cosmx_to_h5mu/main.nf index 775a14f..8b19a8f 100644 --- a/target/nextflow/convert/from_cosmx_to_h5mu/main.nf +++ b/target/nextflow/convert/from_cosmx_to_h5mu/main.nf @@ -3181,12 +3181,6 @@ meta = [ "name" : "openpipeline", "repo" : "openpipelines-bio/openpipeline", "tag" : "2.1.2" - }, - { - "type" : "vsh", - "name" : "openpipeline_incubator", - "repo" : "openpipeline_incubator", - "tag" : "build/main" } ], "links" : { @@ -3337,7 +3331,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_h5mu", "viash_version" : "0.9.4", - "git_commit" : "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8", + "git_commit" : "6f308e6a3cca52f1283fbba734a3cdc858e18e1b", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3358,12 +3352,6 @@ meta = [ "name" : "openpipeline", "repo" : "openpipelines-bio/openpipeline", "tag" : "2.1.2" - }, - { - "type" : "vsh", - "name" : "openpipeline_incubator", - "repo" : "openpipeline_incubator", - "tag" : "build/main" } ], "viash_version" : "0.9.4", 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 e82dfef..1be0996 100644 --- a/target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml +++ b/target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml @@ -124,10 +124,6 @@ repositories: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" -- type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -236,7 +232,7 @@ 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: "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" + git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -251,10 +247,6 @@ package_config: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" - - type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf b/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf index 8e1295e..b4b8968 100644 --- a/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf +++ b/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf @@ -3187,12 +3187,6 @@ meta = [ "name" : "openpipeline", "repo" : "openpipelines-bio/openpipeline", "tag" : "2.1.2" - }, - { - "type" : "vsh", - "name" : "openpipeline_incubator", - "repo" : "openpipeline_incubator", - "tag" : "build/main" } ], "links" : { @@ -3328,7 +3322,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_spatialexperiment", "viash_version" : "0.9.4", - "git_commit" : "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8", + "git_commit" : "6f308e6a3cca52f1283fbba734a3cdc858e18e1b", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3349,12 +3343,6 @@ meta = [ "name" : "openpipeline", "repo" : "openpipelines-bio/openpipeline", "tag" : "2.1.2" - }, - { - "type" : "vsh", - "name" : "openpipeline_incubator", - "repo" : "openpipeline_incubator", - "tag" : "build/main" } ], "viash_version" : "0.9.4", 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 7635e9f..750670c 100644 --- a/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml @@ -102,10 +102,6 @@ repositories: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" -- type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -224,7 +220,7 @@ 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: "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" + git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -239,10 +235,6 @@ package_config: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" - - type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf b/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf index 88385e9..a4eb513 100644 --- a/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf +++ b/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf @@ -3181,12 +3181,6 @@ meta = [ "name" : "openpipeline", "repo" : "openpipelines-bio/openpipeline", "tag" : "2.1.2" - }, - { - "type" : "vsh", - "name" : "openpipeline_incubator", - "repo" : "openpipeline_incubator", - "tag" : "build/main" } ], "links" : { @@ -3336,7 +3330,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_spatialdata_to_h5mu", "viash_version" : "0.9.4", - "git_commit" : "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8", + "git_commit" : "6f308e6a3cca52f1283fbba734a3cdc858e18e1b", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3357,12 +3351,6 @@ meta = [ "name" : "openpipeline", "repo" : "openpipelines-bio/openpipeline", "tag" : "2.1.2" - }, - { - "type" : "vsh", - "name" : "openpipeline_incubator", - "repo" : "openpipeline_incubator", - "tag" : "build/main" } ], "viash_version" : "0.9.4", diff --git a/target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml index 53b3ff9..df798e9 100644 --- a/target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml @@ -120,10 +120,6 @@ repositories: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" -- type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -237,7 +233,7 @@ 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: "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" + git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -252,10 +248,6 @@ package_config: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" - - type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/nextflow/convert/from_xenium_to_h5mu/main.nf b/target/nextflow/convert/from_xenium_to_h5mu/main.nf index 80c4486..db9ac88 100644 --- a/target/nextflow/convert/from_xenium_to_h5mu/main.nf +++ b/target/nextflow/convert/from_xenium_to_h5mu/main.nf @@ -3191,12 +3191,6 @@ meta = [ "name" : "openpipeline", "repo" : "openpipelines-bio/openpipeline", "tag" : "2.1.2" - }, - { - "type" : "vsh", - "name" : "openpipeline_incubator", - "repo" : "openpipeline_incubator", - "tag" : "build/main" } ], "links" : { @@ -3337,7 +3331,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_h5mu", "viash_version" : "0.9.4", - "git_commit" : "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8", + "git_commit" : "6f308e6a3cca52f1283fbba734a3cdc858e18e1b", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3358,12 +3352,6 @@ meta = [ "name" : "openpipeline", "repo" : "openpipelines-bio/openpipeline", "tag" : "2.1.2" - }, - { - "type" : "vsh", - "name" : "openpipeline_incubator", - "repo" : "openpipeline_incubator", - "tag" : "build/main" } ], "viash_version" : "0.9.4", 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 d7df8da..7f774d0 100644 --- a/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml +++ b/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml @@ -200,10 +200,6 @@ repositories: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" -- type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -318,7 +314,7 @@ 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: "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" + git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -333,10 +329,6 @@ package_config: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" - - type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/nextflow/convert/from_xenium_to_spatialdata/main.nf b/target/nextflow/convert/from_xenium_to_spatialdata/main.nf index 7cb2864..fcb33d1 100644 --- a/target/nextflow/convert/from_xenium_to_spatialdata/main.nf +++ b/target/nextflow/convert/from_xenium_to_spatialdata/main.nf @@ -3280,12 +3280,6 @@ meta = [ "name" : "openpipeline", "repo" : "openpipelines-bio/openpipeline", "tag" : "2.1.2" - }, - { - "type" : "vsh", - "name" : "openpipeline_incubator", - "repo" : "openpipeline_incubator", - "tag" : "build/main" } ], "links" : { @@ -3431,7 +3425,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialdata", "viash_version" : "0.9.4", - "git_commit" : "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8", + "git_commit" : "6f308e6a3cca52f1283fbba734a3cdc858e18e1b", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3452,12 +3446,6 @@ meta = [ "name" : "openpipeline", "repo" : "openpipelines-bio/openpipeline", "tag" : "2.1.2" - }, - { - "type" : "vsh", - "name" : "openpipeline_incubator", - "repo" : "openpipeline_incubator", - "tag" : "build/main" } ], "viash_version" : "0.9.4", 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 a7d913a..7e5a537 100644 --- a/target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml +++ b/target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml @@ -114,10 +114,6 @@ repositories: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" -- type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -226,7 +222,7 @@ 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: "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" + git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -241,10 +237,6 @@ package_config: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" - - type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf b/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf index e782c24..3d4f993 100644 --- a/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf +++ b/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf @@ -3176,12 +3176,6 @@ meta = [ "name" : "openpipeline", "repo" : "openpipelines-bio/openpipeline", "tag" : "2.1.2" - }, - { - "type" : "vsh", - "name" : "openpipeline_incubator", - "repo" : "openpipeline_incubator", - "tag" : "build/main" } ], "links" : { @@ -3317,7 +3311,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialexperiment", "viash_version" : "0.9.4", - "git_commit" : "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8", + "git_commit" : "6f308e6a3cca52f1283fbba734a3cdc858e18e1b", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3338,12 +3332,6 @@ meta = [ "name" : "openpipeline", "repo" : "openpipelines-bio/openpipeline", "tag" : "2.1.2" - }, - { - "type" : "vsh", - "name" : "openpipeline_incubator", - "repo" : "openpipeline_incubator", - "tag" : "build/main" } ], "viash_version" : "0.9.4", diff --git a/target/nextflow/filter/subset_cosmx/.config.vsh.yaml b/target/nextflow/filter/subset_cosmx/.config.vsh.yaml index 05c5225..bc0d541 100644 --- a/target/nextflow/filter/subset_cosmx/.config.vsh.yaml +++ b/target/nextflow/filter/subset_cosmx/.config.vsh.yaml @@ -113,10 +113,6 @@ repositories: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" -- type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -231,7 +227,7 @@ build_info: output: "target/nextflow/filter/subset_cosmx" executable: "target/nextflow/filter/subset_cosmx/main.nf" viash_version: "0.9.4" - git_commit: "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" + git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -246,10 +242,6 @@ package_config: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" - - type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/nextflow/filter/subset_cosmx/main.nf b/target/nextflow/filter/subset_cosmx/main.nf index 947a8de..42d40d9 100644 --- a/target/nextflow/filter/subset_cosmx/main.nf +++ b/target/nextflow/filter/subset_cosmx/main.nf @@ -3188,12 +3188,6 @@ meta = [ "name" : "openpipeline", "repo" : "openpipelines-bio/openpipeline", "tag" : "2.1.2" - }, - { - "type" : "vsh", - "name" : "openpipeline_incubator", - "repo" : "openpipeline_incubator", - "tag" : "build/main" } ], "links" : { @@ -3339,7 +3333,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/filter/subset_cosmx", "viash_version" : "0.9.4", - "git_commit" : "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8", + "git_commit" : "6f308e6a3cca52f1283fbba734a3cdc858e18e1b", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3360,12 +3354,6 @@ meta = [ "name" : "openpipeline", "repo" : "openpipelines-bio/openpipeline", "tag" : "2.1.2" - }, - { - "type" : "vsh", - "name" : "openpipeline_incubator", - "repo" : "openpipeline_incubator", - "tag" : "build/main" } ], "viash_version" : "0.9.4", diff --git a/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml b/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml index 4defa46..2a8d69a 100644 --- a/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml +++ b/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml @@ -330,10 +330,6 @@ repositories: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" -- type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" keywords: - "spaceranger" links: @@ -430,7 +426,7 @@ build_info: output: "target/nextflow/mapping/spaceranger_count" executable: "target/nextflow/mapping/spaceranger_count/main.nf" viash_version: "0.9.4" - git_commit: "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" + git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -445,10 +441,6 @@ package_config: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" - - type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/nextflow/mapping/spaceranger_count/main.nf b/target/nextflow/mapping/spaceranger_count/main.nf index 2d8186b..614a33a 100644 --- a/target/nextflow/mapping/spaceranger_count/main.nf +++ b/target/nextflow/mapping/spaceranger_count/main.nf @@ -3433,12 +3433,6 @@ meta = [ "name" : "openpipeline", "repo" : "openpipelines-bio/openpipeline", "tag" : "2.1.2" - }, - { - "type" : "vsh", - "name" : "openpipeline_incubator", - "repo" : "openpipeline_incubator", - "tag" : "build/main" } ], "keywords" : [ @@ -3554,7 +3548,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/mapping/spaceranger_count", "viash_version" : "0.9.4", - "git_commit" : "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8", + "git_commit" : "6f308e6a3cca52f1283fbba734a3cdc858e18e1b", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3575,12 +3569,6 @@ meta = [ "name" : "openpipeline", "repo" : "openpipelines-bio/openpipeline", "tag" : "2.1.2" - }, - { - "type" : "vsh", - "name" : "openpipeline_incubator", - "repo" : "openpipeline_incubator", - "tag" : "build/main" } ], "viash_version" : "0.9.4", 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 dd63a37..4e5668a 100644 --- a/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml +++ b/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml @@ -563,10 +563,6 @@ repositories: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" -- type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" - type: "github" name: "openpipeline_scrublet" repo: "openpipelines-bio/openpipeline" @@ -648,7 +644,7 @@ 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: "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" + git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" dependencies: - "target/dependencies/github/openpipelines-bio/openpipeline/disable-scrublet_build/nextflow/workflows/multiomics/process_samples" @@ -665,10 +661,6 @@ package_config: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" - - type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf b/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf index 8b42d52..5046780 100644 --- a/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf +++ b/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf @@ -3718,12 +3718,6 @@ meta = [ "repo" : "openpipelines-bio/openpipeline", "tag" : "2.1.2" }, - { - "type" : "vsh", - "name" : "openpipeline_incubator", - "repo" : "openpipeline_incubator", - "tag" : "build/main" - }, { "type" : "github", "name" : "openpipeline_scrublet", @@ -3819,7 +3813,7 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/multiomics/spatial_process_samples", "viash_version" : "0.9.4", - "git_commit" : "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8", + "git_commit" : "6f308e6a3cca52f1283fbba734a3cdc858e18e1b", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3840,12 +3834,6 @@ meta = [ "name" : "openpipeline", "repo" : "openpipelines-bio/openpipeline", "tag" : "2.1.2" - }, - { - "type" : "vsh", - "name" : "openpipeline_incubator", - "repo" : "openpipeline_incubator", - "tag" : "build/main" } ], "viash_version" : "0.9.4", diff --git a/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml b/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml index 623eade..cf7a0f9 100644 --- a/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml +++ b/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml @@ -310,10 +310,6 @@ repositories: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" -- type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -391,7 +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: "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8" + git_commit: "6f308e6a3cca52f1283fbba734a3cdc858e18e1b" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" dependencies: - "target/dependencies/github/openpipelines-bio/openpipeline/2.1.2/nextflow/workflows/qc/qc" @@ -408,10 +404,6 @@ package_config: name: "openpipeline" repo: "openpipelines-bio/openpipeline" tag: "2.1.2" - - type: "vsh" - name: "openpipeline_incubator" - repo: "openpipeline_incubator" - tag: "build/main" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/nextflow/workflows/qc/spatial_qc/main.nf b/target/nextflow/workflows/qc/spatial_qc/main.nf index ad923fd..87fefb3 100644 --- a/target/nextflow/workflows/qc/spatial_qc/main.nf +++ b/target/nextflow/workflows/qc/spatial_qc/main.nf @@ -3415,12 +3415,6 @@ meta = [ "name" : "openpipeline", "repo" : "openpipelines-bio/openpipeline", "tag" : "2.1.2" - }, - { - "type" : "vsh", - "name" : "openpipeline_incubator", - "repo" : "openpipeline_incubator", - "tag" : "build/main" } ], "links" : { @@ -3511,7 +3505,7 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/qc/spatial_qc", "viash_version" : "0.9.4", - "git_commit" : "fab3d7dbd86e169a9e3b736c0d7b5bb76b22a1e8", + "git_commit" : "6f308e6a3cca52f1283fbba734a3cdc858e18e1b", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3532,12 +3526,6 @@ meta = [ "name" : "openpipeline", "repo" : "openpipelines-bio/openpipeline", "tag" : "2.1.2" - }, - { - "type" : "vsh", - "name" : "openpipeline_incubator", - "repo" : "openpipeline_incubator", - "tag" : "build/main" } ], "viash_version" : "0.9.4",