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Build branch allow-compressed-output-bundles with version allow-compressed-output-bundles (f951825)

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Build pipeline: openpipelines-bio.openpipeline-spatial.allow-compressed-oumm2z7

Source commit: f951825e3f

Source message: cleanup
This commit is contained in:
CI
2025-08-27 16:53:27 +00:00
parent 008f51517b
commit cfb110c6bb
59 changed files with 452 additions and 115 deletions
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2
target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml
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@@ -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: "2cc934cef9746e6befa3e91c82080bc071294628"
git_commit: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu
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@@ -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="2025-08-27T13:23:38Z"
LABEL org.opencontainers.image.created="2025-08-27T16:31:54Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="2cc934cef9746e6befa3e91c82080bc071294628"
LABEL org.opencontainers.image.revision="f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
LABEL org.opencontainers.image.version="allow-compressed-output-bundles"
VIASHDOCKER

2
target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml
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@@ -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: "2cc934cef9746e6befa3e91c82080bc071294628"
git_commit: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu
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@@ -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="2025-08-27T13:23:38Z"
LABEL org.opencontainers.image.created="2025-08-27T16:31:55Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="2cc934cef9746e6befa3e91c82080bc071294628"
LABEL org.opencontainers.image.revision="f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
LABEL org.opencontainers.image.version="allow-compressed-output-bundles"
VIASHDOCKER

4
target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml
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@@ -98,6 +98,8 @@ resources:
- type: "r_script"
path: "script.R"
is_executable: true
- type: "file"
path: "unzip_archived_folder.R"
- type: "file"
path: "nextflow_labels.config"
dest: "nextflow_labels.config"
@@ -232,7 +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: "2cc934cef9746e6befa3e91c82080bc071294628"
git_commit: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

21
target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment
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@@ -457,9 +457,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("BiocManager", quietly
LABEL org.opencontainers.image.authors="Dorien Roosen"
LABEL org.opencontainers.image.description="Companion container for running component convert from_cosmx_to_spatialexperiment"
LABEL org.opencontainers.image.created="2025-08-27T13:23:37Z"
LABEL org.opencontainers.image.created="2025-08-27T16:31:54Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="2cc934cef9746e6befa3e91c82080bc071294628"
LABEL org.opencontainers.image.revision="f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
LABEL org.opencontainers.image.version="allow-compressed-output-bundles"
VIASHDOCKER
@@ -1221,14 +1221,29 @@ rm(.viash_orig_warn)
### VIASH END
source(paste0(meta\$resources_dir, "/unzip_archived_folder.R"))
if (par\$add_polygon_path == FALSE && par\$add_tx_path == FALSE) {
add_parquet_paths <- FALSE
} else {
add_parquet_paths <- TRUE
}
cosmx_output_bundle <- par\$input
if (grepl("\\\\.zip\$", cosmx_output_bundle)) {
expected_file_patterns <- c(
"*.csv",
"*.parquet"
)
cosmx_output_bundle <- extract_selected_files(
cosmx_output_bundle,
members = expected_file_patterns
)
}
spe <- readCosmxSXE(
dirName = par\$input,
dirName = cosmx_output_bundle,
returnType = "SPE",
countMatPattern = "exprMat_file.csv",
metaDataPattern = "metadata_file.csv",

22
target/executable/convert/from_cosmx_to_spatialexperiment/unzip_archived_folder.R Normal file
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@@ -0,0 +1,22 @@
extract_selected_files <- function(zip_path, members) {
# Create a temporary directory for extraction
temp_dir <- tempfile("unzip_dir_")
dir.create(temp_dir)
# List all files in the archive
all_files <- utils::unzip(zip_path, list = TRUE)$Name
# Find files matching any of the glob patterns in 'members'
selected <- unique(unlist(
lapply(members, function(pattern) {
regex <- glob2rx(pattern)
grep(regex, all_files, value = TRUE)
})
))
# Extract only the selected files
utils::unzip(zip_path, files = selected, exdir = temp_dir)
# Return the path to the extracted folder
file.path(temp_dir)
}

2
target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml
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@@ -224,7 +224,7 @@ build_info:
output: "target/executable/convert/from_h5mu_to_spatialexperiment"
executable: "target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment"
viash_version: "0.9.4"
git_commit: "2cc934cef9746e6befa3e91c82080bc071294628"
git_commit: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment
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@@ -458,9 +458,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
LABEL org.opencontainers.image.authors="Dorien Roosen"
LABEL org.opencontainers.image.description="Companion container for running component convert from_h5mu_to_spatialexperiment"
LABEL org.opencontainers.image.created="2025-08-27T13:23:38Z"
LABEL org.opencontainers.image.created="2025-08-27T16:31:55Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="2cc934cef9746e6befa3e91c82080bc071294628"
LABEL org.opencontainers.image.revision="f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
LABEL org.opencontainers.image.version="allow-compressed-output-bundles"
VIASHDOCKER

2
target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
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@@ -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: "2cc934cef9746e6befa3e91c82080bc071294628"
git_commit: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu
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@@ -459,9 +459,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz"
LABEL org.opencontainers.image.description="Companion container for running component convert from_spatialdata_to_h5mu"
LABEL org.opencontainers.image.created="2025-08-27T13:23:38Z"
LABEL org.opencontainers.image.created="2025-08-27T16:31:55Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="2cc934cef9746e6befa3e91c82080bc071294628"
LABEL org.opencontainers.image.revision="f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
LABEL org.opencontainers.image.version="allow-compressed-output-bundles"
VIASHDOCKER

2
target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml
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@@ -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: "2cc934cef9746e6befa3e91c82080bc071294628"
git_commit: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu
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@@ -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="2025-08-27T13:23:37Z"
LABEL org.opencontainers.image.created="2025-08-27T16:31:54Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="2cc934cef9746e6befa3e91c82080bc071294628"
LABEL org.opencontainers.image.revision="f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
LABEL org.opencontainers.image.version="allow-compressed-output-bundles"
VIASHDOCKER

2
target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml
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@@ -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: "2cc934cef9746e6befa3e91c82080bc071294628"
git_commit: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

12
target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata
View File

@@ -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="2025-08-27T13:23:38Z"
LABEL org.opencontainers.image.created="2025-08-27T16:31:55Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="2cc934cef9746e6befa3e91c82080bc071294628"
LABEL org.opencontainers.image.revision="f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
LABEL org.opencontainers.image.version="allow-compressed-output-bundles"
VIASHDOCKER
@@ -1392,11 +1392,13 @@ from unzip_archived_folder import unzip_archived_folder
logger = setup_logger()
logger.info("Reading in Xenium data...")
if zipfile.is_zipfile(par["input"]):
par["input"] = unzip_archived_folder(par["input"])
if zipfile.is_zipfile(par["input"]):
xenium_output_bundle = unzip_archived_folder(par["input"])
else:
xenium_output_bundle = par["input"]
sdata = xenium(
par["input"],
xenium_output_bundle,
cells_boundaries=par["cells_boundaries"],
nucleus_boundaries=par["nucleus_boundaries"],
cells_as_circles=par["cells_as_circles"],

4
target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml
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@@ -88,6 +88,8 @@ resources:
- type: "r_script"
path: "script.R"
is_executable: true
- type: "file"
path: "unzip_archived_folder.R"
- type: "file"
path: "nextflow_labels.config"
dest: "nextflow_labels.config"
@@ -222,7 +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: "2cc934cef9746e6befa3e91c82080bc071294628"
git_commit: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

21
target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment
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@@ -457,9 +457,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("BiocManager", quietly
LABEL org.opencontainers.image.authors="Dorien Roosen"
LABEL org.opencontainers.image.description="Companion container for running component convert from_xenium_to_spatialexperiment"
LABEL org.opencontainers.image.created="2025-08-27T13:23:37Z"
LABEL org.opencontainers.image.created="2025-08-27T16:31:54Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="2cc934cef9746e6befa3e91c82080bc071294628"
LABEL org.opencontainers.image.revision="f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
LABEL org.opencontainers.image.version="allow-compressed-output-bundles"
VIASHDOCKER
@@ -1195,9 +1195,24 @@ rm(.viash_orig_warn)
### VIASH END
source(paste0(meta\$resources_dir, "/unzip_archived_folder.R"))
xenium_output_bundle <- par\$input
if (grepl("\\\\.zip\$", xenium_output_bundle)) {
expected_file_patterns <- c(
"cell_feature_matrix.h5",
"*.parquet",
"experiment.xenium"
)
xenium_output_bundle <- extract_selected_files(
xenium_output_bundle,
members = expected_file_patterns
)
}
spe <- readXeniumSXE(
dirName = par\$input,
dirName = xenium_output_bundle,
returnType = "SPE",
countMatPattern = "cell_feature_matrix.h5",
metaDataPattern = "cells.parquet",

22
target/executable/convert/from_xenium_to_spatialexperiment/unzip_archived_folder.R Normal file
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@@ -0,0 +1,22 @@
extract_selected_files <- function(zip_path, members) {
# Create a temporary directory for extraction
temp_dir <- tempfile("unzip_dir_")
dir.create(temp_dir)
# List all files in the archive
all_files <- utils::unzip(zip_path, list = TRUE)$Name
# Find files matching any of the glob patterns in 'members'
selected <- unique(unlist(
lapply(members, function(pattern) {
regex <- glob2rx(pattern)
grep(regex, all_files, value = TRUE)
})
))
# Extract only the selected files
utils::unzip(zip_path, files = selected, exdir = temp_dir)
# Return the path to the extracted folder
file.path(temp_dir)
}

2
target/executable/filter/subset_cosmx/.config.vsh.yaml
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@@ -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: "2cc934cef9746e6befa3e91c82080bc071294628"
git_commit: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/executable/filter/subset_cosmx/subset_cosmx
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@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz"
LABEL org.opencontainers.image.description="Companion container for running component filter subset_cosmx"
LABEL org.opencontainers.image.created="2025-08-27T13:23:37Z"
LABEL org.opencontainers.image.created="2025-08-27T16:31:54Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="2cc934cef9746e6befa3e91c82080bc071294628"
LABEL org.opencontainers.image.revision="f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
LABEL org.opencontainers.image.version="allow-compressed-output-bundles"
VIASHDOCKER

2
target/executable/mapping/spaceranger_count/.config.vsh.yaml
View File

@@ -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: "2cc934cef9746e6befa3e91c82080bc071294628"
git_commit: "f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"

4
target/executable/mapping/spaceranger_count/spaceranger_count
View File

@@ -453,9 +453,9 @@ apt upgrade -y && apt install -y procps && rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.authors="Jakub Majercik"
LABEL org.opencontainers.image.description="Companion container for running component mapping spaceranger_count"
LABEL org.opencontainers.image.created="2025-08-27T13:23:37Z"
LABEL org.opencontainers.image.created="2025-08-27T16:31:54Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="2cc934cef9746e6befa3e91c82080bc071294628"
LABEL org.opencontainers.image.revision="f951825e3f6f7d9ad09b4803220f5af99fe4ae14"
LABEL org.opencontainers.image.version="allow-compressed-output-bundles"
VIASHDOCKER