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Build branch v0.1 with version v0.1 (420b610)

Browse Source 
Build pipeline: openpipelines-bio.openpipeline-spatial.v0.1-rwpq2

Source commit: 420b610b04

Source message: Merge pull request #18 from openpipelines-bio/update-op-dependencies

Update OP dependency version
This commit is contained in:
CI
2025-08-25 12:10:43 +00:00
parent 21602a0829
commit e3029375b3
364 changed files with 3095 additions and 18895 deletions
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10
target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "from_cells2stats_to_h5mu"
namespace: "convert"
version: "v0.1.0"
version: "v0.1"
authors:
- name: "Dorien Roosen"
roles:
@@ -256,7 +256,7 @@ engines:
id: "docker"
image: "python:3.13-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.1.0"
target_tag: "v0.1"
namespace_separator: "/"
setup:
- type: "apt"
@@ -290,11 +290,11 @@ 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: "963107088819638e9e15d4f413c0a763dc81a192"
git_commit: "420b610b045c138f07475a1af39529f233d9af5a"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "v0.1"
info:
test_resources:
- type: "s3"
@@ -314,7 +314,7 @@ package_config:
)'"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
- ".engines[.type == 'docker'].target_tag := 'v0.1'"
organization: "vsh"
links:
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

14
target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# from_cells2stats_to_h5mu v0.1.0
# from_cells2stats_to_h5mu v0.1
#
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ 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="2025-08-25T08:17:05Z"
LABEL org.opencontainers.image.created="2025-08-25T11:47:08Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="963107088819638e9e15d4f413c0a763dc81a192"
LABEL org.opencontainers.image.version="v0.1.0"
LABEL org.opencontainers.image.revision="420b610b045c138f07475a1af39529f233d9af5a"
LABEL org.opencontainers.image.version="v0.1"
VIASHDOCKER
fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "from_cells2stats_to_h5mu v0.1.0"
echo "from_cells2stats_to_h5mu v0.1"
echo ""
echo "Convert spatial data resulting from Aviti Teton sequencers that have been"
echo "processed by the Element Biosciences cells2stats workflow to H5MU format."
@@ -722,7 +722,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "from_cells2stats_to_h5mu v0.1.0"
echo "from_cells2stats_to_h5mu v0.1"
exit
;;
--input)
@@ -923,7 +923,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/convert/from_cells2stats_to_h5mu:v0.1.0'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/convert/from_cells2stats_to_h5mu:v0.1'
fi
# print dockerfile

10
target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "from_cosmx_to_h5mu"
namespace: "convert"
version: "v0.1.0"
version: "v0.1"
authors:
- name: "Dorien Roosen"
roles:
@@ -184,7 +184,7 @@ engines:
id: "docker"
image: "python:3.12-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.1.0"
target_tag: "v0.1"
namespace_separator: "/"
setup:
- type: "apt"
@@ -225,11 +225,11 @@ 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: "963107088819638e9e15d4f413c0a763dc81a192"
git_commit: "420b610b045c138f07475a1af39529f233d9af5a"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "v0.1"
info:
test_resources:
- type: "s3"
@@ -249,7 +249,7 @@ package_config:
)'"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
- ".engines[.type == 'docker'].target_tag := 'v0.1'"
organization: "vsh"
links:
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

14
target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# from_cosmx_to_h5mu v0.1.0
# from_cosmx_to_h5mu v0.1
#
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ 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="2025-08-25T08:17:06Z"
LABEL org.opencontainers.image.created="2025-08-25T11:47:10Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="963107088819638e9e15d4f413c0a763dc81a192"
LABEL org.opencontainers.image.version="v0.1.0"
LABEL org.opencontainers.image.revision="420b610b045c138f07475a1af39529f233d9af5a"
LABEL org.opencontainers.image.version="v0.1"
VIASHDOCKER
fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "from_cosmx_to_h5mu v0.1.0"
echo "from_cosmx_to_h5mu v0.1"
echo ""
echo "Converts the output from NanoString experiment into a MuData objcet."
echo " - \`<dataset_id>_exprMat_file.csv\`: File containing the counts."
@@ -658,7 +658,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "from_cosmx_to_h5mu v0.1.0"
echo "from_cosmx_to_h5mu v0.1"
exit
;;
--input)
@@ -805,7 +805,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/convert/from_cosmx_to_h5mu:v0.1.0'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/convert/from_cosmx_to_h5mu:v0.1'
fi
# print dockerfile

10
target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "from_cosmx_to_spatialexperiment"
namespace: "convert"
version: "v0.1.0"
version: "v0.1"
authors:
- name: "Dorien Roosen"
roles:
@@ -202,7 +202,7 @@ engines:
id: "docker"
image: "rocker/r2u:24.04"
target_registry: "images.viash-hub.com"
target_tag: "v0.1.0"
target_tag: "v0.1"
namespace_separator: "/"
setup:
- type: "apt"
@@ -232,11 +232,11 @@ 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: "963107088819638e9e15d4f413c0a763dc81a192"
git_commit: "420b610b045c138f07475a1af39529f233d9af5a"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "v0.1"
info:
test_resources:
- type: "s3"
@@ -256,7 +256,7 @@ package_config:
)'"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
- ".engines[.type == 'docker'].target_tag := 'v0.1'"
organization: "vsh"
links:
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

14
target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# from_cosmx_to_spatialexperiment v0.1.0
# from_cosmx_to_spatialexperiment v0.1
#
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -457,10 +457,10 @@ 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="2025-08-25T08:17:05Z"
LABEL org.opencontainers.image.created="2025-08-25T11:47:09Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="963107088819638e9e15d4f413c0a763dc81a192"
LABEL org.opencontainers.image.version="v0.1.0"
LABEL org.opencontainers.image.revision="420b610b045c138f07475a1af39529f233d9af5a"
LABEL org.opencontainers.image.version="v0.1"
VIASHDOCKER
fi
@@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "from_cosmx_to_spatialexperiment v0.1.0"
echo "from_cosmx_to_spatialexperiment v0.1"
echo ""
echo "Creates a SpatialExperiment object from the downloaded unzipped CosMx directory"
echo "for Nanostring"
@@ -678,7 +678,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "from_cosmx_to_spatialexperiment v0.1.0"
echo "from_cosmx_to_spatialexperiment v0.1"
exit
;;
--input)
@@ -853,7 +853,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/convert/from_cosmx_to_spatialexperiment:v0.1.0'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/convert/from_cosmx_to_spatialexperiment:v0.1'
fi
# print dockerfile

10
target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "from_h5mu_to_spatialexperiment"
namespace: "convert"
version: "v0.1.0"
version: "v0.1"
authors:
- name: "Dorien Roosen"
roles:
@@ -171,7 +171,7 @@ engines:
id: "docker"
image: "rocker/r2u:22.04"
target_registry: "images.viash-hub.com"
target_tag: "v0.1.0"
target_tag: "v0.1"
namespace_separator: "/"
setup:
- type: "apt"
@@ -224,11 +224,11 @@ 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: "963107088819638e9e15d4f413c0a763dc81a192"
git_commit: "420b610b045c138f07475a1af39529f233d9af5a"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "v0.1"
info:
test_resources:
- type: "s3"
@@ -248,7 +248,7 @@ package_config:
)'"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
- ".engines[.type == 'docker'].target_tag := 'v0.1'"
organization: "vsh"
links:
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

14
target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# from_h5mu_to_spatialexperiment v0.1.0
# from_h5mu_to_spatialexperiment v0.1
#
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ 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="2025-08-25T08:17:06Z"
LABEL org.opencontainers.image.created="2025-08-25T11:47:09Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="963107088819638e9e15d4f413c0a763dc81a192"
LABEL org.opencontainers.image.version="v0.1.0"
LABEL org.opencontainers.image.revision="420b610b045c138f07475a1af39529f233d9af5a"
LABEL org.opencontainers.image.version="v0.1"
VIASHDOCKER
fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "from_h5mu_to_spatialexperiment v0.1.0"
echo "from_h5mu_to_spatialexperiment v0.1"
echo ""
echo "Converts an h5mu file into a SpatialExperiment object."
echo ""
@@ -650,7 +650,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "from_h5mu_to_spatialexperiment v0.1.0"
echo "from_h5mu_to_spatialexperiment v0.1"
exit
;;
--input)
@@ -797,7 +797,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/convert/from_h5mu_to_spatialexperiment:v0.1.0'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/convert/from_h5mu_to_spatialexperiment:v0.1'
fi
# print dockerfile

10
target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "from_spatialdata_to_h5mu"
namespace: "convert"
version: "v0.1.0"
version: "v0.1"
authors:
- name: "Dorien Roosen"
roles:
@@ -180,7 +180,7 @@ engines:
id: "docker"
image: "python:3.12-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.1.0"
target_tag: "v0.1"
namespace_separator: "/"
setup:
- type: "apt"
@@ -220,11 +220,11 @@ 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: "963107088819638e9e15d4f413c0a763dc81a192"
git_commit: "420b610b045c138f07475a1af39529f233d9af5a"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "v0.1"
info:
test_resources:
- type: "s3"
@@ -244,7 +244,7 @@ package_config:
)'"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
- ".engines[.type == 'docker'].target_tag := 'v0.1'"
organization: "vsh"
links:
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

14
target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# from_spatialdata_to_h5mu v0.1.0
# from_spatialdata_to_h5mu v0.1
#
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ 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="2025-08-25T08:17:05Z"
LABEL org.opencontainers.image.created="2025-08-25T11:47:09Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="963107088819638e9e15d4f413c0a763dc81a192"
LABEL org.opencontainers.image.version="v0.1.0"
LABEL org.opencontainers.image.revision="420b610b045c138f07475a1af39529f233d9af5a"
LABEL org.opencontainers.image.version="v0.1"
VIASHDOCKER
fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "from_spatialdata_to_h5mu v0.1.0"
echo "from_spatialdata_to_h5mu v0.1"
echo ""
echo "Reads in the Tables field stored in a SpatialData object and converts it to an"
echo "h5mu file."
@@ -651,7 +651,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "from_spatialdata_to_h5mu v0.1.0"
echo "from_spatialdata_to_h5mu v0.1"
exit
;;
--input)
@@ -798,7 +798,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/convert/from_spatialdata_to_h5mu:v0.1.0'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/convert/from_spatialdata_to_h5mu:v0.1'
fi
# print dockerfile

10
target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "from_xenium_to_h5mu"
namespace: "convert"
version: "v0.1.0"
version: "v0.1"
authors:
- name: "Dorien Roosen"
roles:
@@ -198,7 +198,7 @@ engines:
id: "docker"
image: "python:3.12-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.1.0"
target_tag: "v0.1"
namespace_separator: "/"
setup:
- type: "apt"
@@ -233,11 +233,11 @@ 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: "963107088819638e9e15d4f413c0a763dc81a192"
git_commit: "420b610b045c138f07475a1af39529f233d9af5a"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "v0.1"
info:
test_resources:
- type: "s3"
@@ -257,7 +257,7 @@ package_config:
)'"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
- ".engines[.type == 'docker'].target_tag := 'v0.1'"
organization: "vsh"
links:
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

14
target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# from_xenium_to_h5mu v0.1.0
# from_xenium_to_h5mu v0.1
#
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ 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="2025-08-25T08:17:05Z"
LABEL org.opencontainers.image.created="2025-08-25T11:47:09Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="963107088819638e9e15d4f413c0a763dc81a192"
LABEL org.opencontainers.image.version="v0.1.0"
LABEL org.opencontainers.image.revision="420b610b045c138f07475a1af39529f233d9af5a"
LABEL org.opencontainers.image.version="v0.1"
VIASHDOCKER
fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "from_xenium_to_h5mu v0.1.0"
echo "from_xenium_to_h5mu v0.1"
echo ""
echo "Converts the output from Xenium to a single .h5mu file, where the count matrix"
echo "is written to the \`rna\` modality."
@@ -670,7 +670,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "from_xenium_to_h5mu v0.1.0"
echo "from_xenium_to_h5mu v0.1"
exit
;;
--input)
@@ -839,7 +839,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/convert/from_xenium_to_h5mu:v0.1.0'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/convert/from_xenium_to_h5mu:v0.1'
fi
# print dockerfile

10
target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "from_xenium_to_spatialdata"
namespace: "convert"
version: "v0.1.0"
version: "v0.1"
authors:
- name: "Dorien Roosen"
roles:
@@ -278,7 +278,7 @@ engines:
id: "docker"
image: "python:3.12-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.1.0"
target_tag: "v0.1"
namespace_separator: "/"
setup:
- type: "apt"
@@ -314,11 +314,11 @@ 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: "963107088819638e9e15d4f413c0a763dc81a192"
git_commit: "420b610b045c138f07475a1af39529f233d9af5a"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "v0.1"
info:
test_resources:
- type: "s3"
@@ -338,7 +338,7 @@ package_config:
)'"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
- ".engines[.type == 'docker'].target_tag := 'v0.1'"
organization: "vsh"
links:
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

14
target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# from_xenium_to_spatialdata v0.1.0
# from_xenium_to_spatialdata v0.1
#
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ 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="2025-08-25T08:17:06Z"
LABEL org.opencontainers.image.created="2025-08-25T11:47:09Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="963107088819638e9e15d4f413c0a763dc81a192"
LABEL org.opencontainers.image.version="v0.1.0"
LABEL org.opencontainers.image.revision="420b610b045c138f07475a1af39529f233d9af5a"
LABEL org.opencontainers.image.version="v0.1"
VIASHDOCKER
fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "from_xenium_to_spatialdata v0.1.0"
echo "from_xenium_to_spatialdata v0.1"
echo ""
echo "Converts the output from 10X Genomics Xenium dataset into a SpatialData objcet."
echo "By default, the following files will be converted:"
@@ -711,7 +711,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "from_xenium_to_spatialdata v0.1.0"
echo "from_xenium_to_spatialdata v0.1"
exit
;;
--input)
@@ -951,7 +951,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/convert/from_xenium_to_spatialdata:v0.1.0'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/convert/from_xenium_to_spatialdata:v0.1'
fi
# print dockerfile

10
target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "from_xenium_to_spatialexperiment"
namespace: "convert"
version: "v0.1.0"
version: "v0.1"
authors:
- name: "Dorien Roosen"
roles:
@@ -192,7 +192,7 @@ engines:
id: "docker"
image: "rocker/r2u:24.04"
target_registry: "images.viash-hub.com"
target_tag: "v0.1.0"
target_tag: "v0.1"
namespace_separator: "/"
setup:
- type: "apt"
@@ -222,11 +222,11 @@ 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: "963107088819638e9e15d4f413c0a763dc81a192"
git_commit: "420b610b045c138f07475a1af39529f233d9af5a"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "v0.1"
info:
test_resources:
- type: "s3"
@@ -246,7 +246,7 @@ package_config:
)'"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
- ".engines[.type == 'docker'].target_tag := 'v0.1'"
organization: "vsh"
links:
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

14
target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# from_xenium_to_spatialexperiment v0.1.0
# from_xenium_to_spatialexperiment v0.1
#
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -457,10 +457,10 @@ 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="2025-08-25T08:17:05Z"
LABEL org.opencontainers.image.created="2025-08-25T11:47:09Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="963107088819638e9e15d4f413c0a763dc81a192"
LABEL org.opencontainers.image.version="v0.1.0"
LABEL org.opencontainers.image.revision="420b610b045c138f07475a1af39529f233d9af5a"
LABEL org.opencontainers.image.version="v0.1"
VIASHDOCKER
fi
@@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "from_xenium_to_spatialexperiment v0.1.0"
echo "from_xenium_to_spatialexperiment v0.1"
echo ""
echo "Creates a SpatialExperiment object from the downloaded unzipped Xenium Output"
echo "Bundle directory"
@@ -673,7 +673,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "from_xenium_to_spatialexperiment v0.1.0"
echo "from_xenium_to_spatialexperiment v0.1"
exit
;;
--input)
@@ -837,7 +837,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/convert/from_xenium_to_spatialexperiment:v0.1.0'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/convert/from_xenium_to_spatialexperiment:v0.1'
fi
# print dockerfile