Build branch allow-compressed-output-bundles with version allow-compressed-output-bundles (56c413e)

Build pipeline: openpipelines-bio.openpipeline-spatial.allow-compressed-ourtbs9 Source commit: 56c413edcb Source message: Merge remote-tracking branch 'origin/main' into allow-compressed-output-bundles
2025-08-28 07:30:51 +00:00
parent cfb110c6bb
commit b27f3f2210
46 changed files with 97 additions and 55 deletions
--- a/.gitignore
+++ b/.gitignore
@@ -58,7 +58,6 @@ trace*.txt
 .vscode/settings.json

 # linting
-ruff.toml
 renv.lock
 .Rprofile
 renv/
--- a/ruff.toml
+++ b/ruff.toml
@@ -0,0 +1,43 @@
+# Exclude a variety of commonly ignored directories.
+exclude = [
+    ".git",
+    ".pyenv",
+    ".pytest_cache",
+    ".ruff_cache",
+    ".venv",
+    ".vscode",
+    "__pypackages__",
+    "_build",
+    "build",
+    "dist",
+    "node_modules",
+    "site-packages",
+]
+
+builtins = ["meta"]
+
+
+
+
+[format]
+# Like Black, use double quotes for strings.
+quote-style = "double"
+
+# Like Black, indent with spaces, rather than tabs.
+indent-style = "space"
+
+# Like Black, respect magic trailing commas.
+skip-magic-trailing-comma = false
+
+# Like Black, automatically detect the appropriate line ending.
+line-ending = "auto"
+
+[lint.flake8-pytest-style]
+fixture-parentheses = false
+mark-parentheses = false
+
+[lint]
+ignore = [
+  # module level import not at top of file
+  "E402"
+]
--- a/target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml
@@ -296,7 +296,7 @@ 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: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+  git_commit: "56c413edcb8630cf4e6df89a39589c44dbb53d53"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- 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="2025-08-27T16:31:54Z"
+LABEL org.opencontainers.image.created="2025-08-28T07:09:08Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+LABEL org.opencontainers.image.revision="56c413edcb8630cf4e6df89a39589c44dbb53d53"
 LABEL org.opencontainers.image.version="allow-compressed-output-bundles"

 VIASHDOCKER
--- a/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml
@@ -231,7 +231,7 @@ 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: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+  git_commit: "56c413edcb8630cf4e6df89a39589c44dbb53d53"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- 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="2025-08-27T16:31:55Z"
+LABEL org.opencontainers.image.created="2025-08-28T07:09:09Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+LABEL org.opencontainers.image.revision="56c413edcb8630cf4e6df89a39589c44dbb53d53"
 LABEL org.opencontainers.image.version="allow-compressed-output-bundles"

 VIASHDOCKER
--- a/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml
+++ b/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml
@@ -234,7 +234,7 @@ build_info:
  output: "target/executable/convert/from_cosmx_to_spatialexperiment"
  executable: "target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment"
  viash_version: "0.9.4"
-  git_commit: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+  git_commit: "56c413edcb8630cf4e6df89a39589c44dbb53d53"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- 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="2025-08-27T16:31:54Z"
+LABEL org.opencontainers.image.created="2025-08-28T07:09:08Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+LABEL org.opencontainers.image.revision="56c413edcb8630cf4e6df89a39589c44dbb53d53"
 LABEL org.opencontainers.image.version="allow-compressed-output-bundles"

 VIASHDOCKER
--- a/target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml
+++ b/target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml
@@ -224,7 +224,7 @@ build_info:
  output: "target/executable/convert/from_h5mu_to_spatialexperiment"
  executable: "target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment"
  viash_version: "0.9.4"
-  git_commit: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+  git_commit: "56c413edcb8630cf4e6df89a39589c44dbb53d53"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment
+++ b/target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment
@@ -458,9 +458,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_h5mu_to_spatialexperiment"
-LABEL org.opencontainers.image.created="2025-08-27T16:31:55Z"
+LABEL org.opencontainers.image.created="2025-08-28T07:09:08Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+LABEL org.opencontainers.image.revision="56c413edcb8630cf4e6df89a39589c44dbb53d53"
 LABEL org.opencontainers.image.version="allow-compressed-output-bundles"

 VIASHDOCKER
--- a/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
@@ -220,7 +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: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+  git_commit: "56c413edcb8630cf4e6df89a39589c44dbb53d53"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- 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="2025-08-27T16:31:55Z"
+LABEL org.opencontainers.image.created="2025-08-28T07:09:08Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+LABEL org.opencontainers.image.revision="56c413edcb8630cf4e6df89a39589c44dbb53d53"
 LABEL org.opencontainers.image.version="allow-compressed-output-bundles"

 VIASHDOCKER
--- a/target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml
@@ -239,7 +239,7 @@ 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: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+  git_commit: "56c413edcb8630cf4e6df89a39589c44dbb53d53"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- 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="2025-08-27T16:31:54Z"
+LABEL org.opencontainers.image.created="2025-08-28T07:09:08Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+LABEL org.opencontainers.image.revision="56c413edcb8630cf4e6df89a39589c44dbb53d53"
 LABEL org.opencontainers.image.version="allow-compressed-output-bundles"

 VIASHDOCKER
--- a/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml
+++ b/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml
@@ -320,7 +320,7 @@ 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: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+  git_commit: "56c413edcb8630cf4e6df89a39589c44dbb53d53"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- 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="2025-08-27T16:31:55Z"
+LABEL org.opencontainers.image.created="2025-08-28T07:09:08Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+LABEL org.opencontainers.image.revision="56c413edcb8630cf4e6df89a39589c44dbb53d53"
 LABEL org.opencontainers.image.version="allow-compressed-output-bundles"

 VIASHDOCKER
--- a/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml
+++ b/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml
@@ -224,7 +224,7 @@ 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: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+  git_commit: "56c413edcb8630cf4e6df89a39589c44dbb53d53"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- 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="2025-08-27T16:31:54Z"
+LABEL org.opencontainers.image.created="2025-08-28T07:09:07Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+LABEL org.opencontainers.image.revision="56c413edcb8630cf4e6df89a39589c44dbb53d53"
 LABEL org.opencontainers.image.version="allow-compressed-output-bundles"

 VIASHDOCKER
--- a/target/executable/filter/subset_cosmx/.config.vsh.yaml
+++ b/target/executable/filter/subset_cosmx/.config.vsh.yaml
@@ -227,7 +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: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+  git_commit: "56c413edcb8630cf4e6df89a39589c44dbb53d53"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- 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="2025-08-27T16:31:54Z"
+LABEL org.opencontainers.image.created="2025-08-28T07:09:07Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+LABEL org.opencontainers.image.revision="56c413edcb8630cf4e6df89a39589c44dbb53d53"
 LABEL org.opencontainers.image.version="allow-compressed-output-bundles"

 VIASHDOCKER
--- a/target/executable/mapping/spaceranger_count/.config.vsh.yaml
+++ b/target/executable/mapping/spaceranger_count/.config.vsh.yaml
@@ -426,7 +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: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+  git_commit: "56c413edcb8630cf4e6df89a39589c44dbb53d53"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- 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="2025-08-27T16:31:54Z"
+LABEL org.opencontainers.image.created="2025-08-28T07:09:07Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
-LABEL org.opencontainers.image.revision="f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+LABEL org.opencontainers.image.revision="56c413edcb8630cf4e6df89a39589c44dbb53d53"
 LABEL org.opencontainers.image.version="allow-compressed-output-bundles"

 VIASHDOCKER
--- a/target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml
@@ -296,7 +296,7 @@ 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: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+  git_commit: "56c413edcb8630cf4e6df89a39589c44dbb53d53"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/convert/from_cells2stats_to_h5mu/main.nf
+++ b/target/nextflow/convert/from_cells2stats_to_h5mu/main.nf
@@ -3393,7 +3393,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_cells2stats_to_h5mu",
    "viash_version" : "0.9.4",
-    "git_commit" : "f951825e3f6f7d9ad09b4803220f5af99fe4ae14",
+    "git_commit" : "56c413edcb8630cf4e6df89a39589c44dbb53d53",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml
@@ -231,7 +231,7 @@ 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: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+  git_commit: "56c413edcb8630cf4e6df89a39589c44dbb53d53"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/convert/from_cosmx_to_h5mu/main.nf
+++ b/target/nextflow/convert/from_cosmx_to_h5mu/main.nf
@@ -3342,7 +3342,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_h5mu",
    "viash_version" : "0.9.4",
-    "git_commit" : "f951825e3f6f7d9ad09b4803220f5af99fe4ae14",
+    "git_commit" : "56c413edcb8630cf4e6df89a39589c44dbb53d53",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml
+++ b/target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml
@@ -234,7 +234,7 @@ build_info:
  output: "target/nextflow/convert/from_cosmx_to_spatialexperiment"
  executable: "target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf"
  viash_version: "0.9.4"
-  git_commit: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+  git_commit: "56c413edcb8630cf4e6df89a39589c44dbb53d53"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf
+++ b/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf
@@ -3326,7 +3326,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_spatialexperiment",
    "viash_version" : "0.9.4",
-    "git_commit" : "f951825e3f6f7d9ad09b4803220f5af99fe4ae14",
+    "git_commit" : "56c413edcb8630cf4e6df89a39589c44dbb53d53",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml
+++ b/target/nextflow/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml
@@ -224,7 +224,7 @@ build_info:
  output: "target/nextflow/convert/from_h5mu_to_spatialexperiment"
  executable: "target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf"
  viash_version: "0.9.4"
-  git_commit: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+  git_commit: "56c413edcb8630cf4e6df89a39589c44dbb53d53"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf
+++ b/target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf
@@ -3332,7 +3332,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_h5mu_to_spatialexperiment",
    "viash_version" : "0.9.4",
-    "git_commit" : "f951825e3f6f7d9ad09b4803220f5af99fe4ae14",
+    "git_commit" : "56c413edcb8630cf4e6df89a39589c44dbb53d53",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
@@ -220,7 +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: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+  git_commit: "56c413edcb8630cf4e6df89a39589c44dbb53d53"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf
+++ b/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf
@@ -3330,7 +3330,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_spatialdata_to_h5mu",
    "viash_version" : "0.9.4",
-    "git_commit" : "f951825e3f6f7d9ad09b4803220f5af99fe4ae14",
+    "git_commit" : "56c413edcb8630cf4e6df89a39589c44dbb53d53",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml
@@ -239,7 +239,7 @@ 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: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+  git_commit: "56c413edcb8630cf4e6df89a39589c44dbb53d53"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/convert/from_xenium_to_h5mu/main.nf
+++ b/target/nextflow/convert/from_xenium_to_h5mu/main.nf
@@ -3342,7 +3342,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_h5mu",
    "viash_version" : "0.9.4",
-    "git_commit" : "f951825e3f6f7d9ad09b4803220f5af99fe4ae14",
+    "git_commit" : "56c413edcb8630cf4e6df89a39589c44dbb53d53",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml
+++ b/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml
@@ -320,7 +320,7 @@ 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: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+  git_commit: "56c413edcb8630cf4e6df89a39589c44dbb53d53"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/convert/from_xenium_to_spatialdata/main.nf
+++ b/target/nextflow/convert/from_xenium_to_spatialdata/main.nf
@@ -3436,7 +3436,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialdata",
    "viash_version" : "0.9.4",
-    "git_commit" : "f951825e3f6f7d9ad09b4803220f5af99fe4ae14",
+    "git_commit" : "56c413edcb8630cf4e6df89a39589c44dbb53d53",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml
+++ b/target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml
@@ -224,7 +224,7 @@ 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: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+  git_commit: "56c413edcb8630cf4e6df89a39589c44dbb53d53"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf
+++ b/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf
@@ -3315,7 +3315,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialexperiment",
    "viash_version" : "0.9.4",
-    "git_commit" : "f951825e3f6f7d9ad09b4803220f5af99fe4ae14",
+    "git_commit" : "56c413edcb8630cf4e6df89a39589c44dbb53d53",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/filter/subset_cosmx/.config.vsh.yaml
+++ b/target/nextflow/filter/subset_cosmx/.config.vsh.yaml
@@ -227,7 +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: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+  git_commit: "56c413edcb8630cf4e6df89a39589c44dbb53d53"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/filter/subset_cosmx/main.nf
+++ b/target/nextflow/filter/subset_cosmx/main.nf
@@ -3333,7 +3333,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/filter/subset_cosmx",
    "viash_version" : "0.9.4",
-    "git_commit" : "f951825e3f6f7d9ad09b4803220f5af99fe4ae14",
+    "git_commit" : "56c413edcb8630cf4e6df89a39589c44dbb53d53",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml
+++ b/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml
@@ -426,7 +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: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+  git_commit: "56c413edcb8630cf4e6df89a39589c44dbb53d53"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
 package_config:
  name: "openpipeline_spatial"
--- a/target/nextflow/mapping/spaceranger_count/main.nf
+++ b/target/nextflow/mapping/spaceranger_count/main.nf
@@ -3548,7 +3548,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "/workdir/root/repo/target/nextflow/mapping/spaceranger_count",
    "viash_version" : "0.9.4",
-    "git_commit" : "f951825e3f6f7d9ad09b4803220f5af99fe4ae14",
+    "git_commit" : "56c413edcb8630cf4e6df89a39589c44dbb53d53",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml
+++ b/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml
@@ -640,7 +640,7 @@ build_info:
  output: "target/nextflow/workflows/multiomics/spatial_process_samples"
  executable: "target/nextflow/workflows/multiomics/spatial_process_samples/main.nf"
  viash_version: "0.9.4"
-  git_commit: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+  git_commit: "56c413edcb8630cf4e6df89a39589c44dbb53d53"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
  dependencies:
  - "target/dependencies/vsh/vsh/openpipeline/v3.0.0/nextflow/workflows/multiomics/process_samples"
--- a/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf
+++ b/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf
@@ -3807,7 +3807,7 @@ meta = [
    "engine" : "native",
    "output" : "/workdir/root/repo/target/nextflow/workflows/multiomics/spatial_process_samples",
    "viash_version" : "0.9.4",
-    "git_commit" : "f951825e3f6f7d9ad09b4803220f5af99fe4ae14",
+    "git_commit" : "56c413edcb8630cf4e6df89a39589c44dbb53d53",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {
--- a/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml
+++ b/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml
@@ -387,7 +387,7 @@ build_info:
  output: "target/nextflow/workflows/qc/spatial_qc"
  executable: "target/nextflow/workflows/qc/spatial_qc/main.nf"
  viash_version: "0.9.4"
-  git_commit: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
+  git_commit: "56c413edcb8630cf4e6df89a39589c44dbb53d53"
  git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
  dependencies:
  - "target/dependencies/vsh/vsh/openpipeline/v3.0.0/nextflow/workflows/qc/qc"
--- a/target/nextflow/workflows/qc/spatial_qc/main.nf
+++ b/target/nextflow/workflows/qc/spatial_qc/main.nf
@@ -3505,7 +3505,7 @@ meta = [
    "engine" : "native",
    "output" : "/workdir/root/repo/target/nextflow/workflows/qc/spatial_qc",
    "viash_version" : "0.9.4",
-    "git_commit" : "f951825e3f6f7d9ad09b4803220f5af99fe4ae14",
+    "git_commit" : "56c413edcb8630cf4e6df89a39589c44dbb53d53",
    "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
  },
  "package_config" : {