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Build branch update-op-dependencies with version update-op-dependencies (793ba55)

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Build pipeline: openpipelines-bio.openpipeline-spatial.update-op-dependenczn6fv

Source commit: 793ba55aab

Source message: cleanup
This commit is contained in:
CI
2025-08-25 11:20:59 +00:00
parent 606bf32ee4
commit f8513d1379
58 changed files with 271 additions and 272 deletions
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2
CHANGELOG.md
View File

@@ -1,4 +1,4 @@
# openpipeline_spatial 0.1.0
# openpipeline_spatial 0.0.0
## NEW FUNCTIONALITY

1
_viash.yaml
View File

@@ -1,4 +1,3 @@
version: v0.1.0
viash_version: 0.9.4
source: src

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: "update-op-dependencies"
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: "update-op-dependencies"
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: "ef8f9ab8bdb22201fe1c1f954607454d5035f230"
git_commit: "793ba55aab5fa80364fa94d2936582f7ac98da0c"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "update-op-dependencies"
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 := 'update-op-dependencies'"
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 update-op-dependencies
#
# 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="2025-08-25T09:57:38Z"
LABEL org.opencontainers.image.created="2025-08-25T10:58:04Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="ef8f9ab8bdb22201fe1c1f954607454d5035f230"
LABEL org.opencontainers.image.version="v0.1.0"
LABEL org.opencontainers.image.revision="793ba55aab5fa80364fa94d2936582f7ac98da0c"
LABEL org.opencontainers.image.version="update-op-dependencies"
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 update-op-dependencies"
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 [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "from_cells2stats_to_h5mu v0.1.0"
echo "from_cells2stats_to_h5mu update-op-dependencies"
exit
;;
--input)
@@ -923,7 +923,7 @@ if [[ "$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:update-op-dependencies'
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: "update-op-dependencies"
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: "update-op-dependencies"
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: "ef8f9ab8bdb22201fe1c1f954607454d5035f230"
git_commit: "793ba55aab5fa80364fa94d2936582f7ac98da0c"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "update-op-dependencies"
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 := 'update-op-dependencies'"
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 update-op-dependencies
#
# 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="2025-08-25T09:57:39Z"
LABEL org.opencontainers.image.created="2025-08-25T10:58:05Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="ef8f9ab8bdb22201fe1c1f954607454d5035f230"
LABEL org.opencontainers.image.version="v0.1.0"
LABEL org.opencontainers.image.revision="793ba55aab5fa80364fa94d2936582f7ac98da0c"
LABEL org.opencontainers.image.version="update-op-dependencies"
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 update-op-dependencies"
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 [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "from_cosmx_to_h5mu v0.1.0"
echo "from_cosmx_to_h5mu update-op-dependencies"
exit
;;
--input)
@@ -805,7 +805,7 @@ if [[ "$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:update-op-dependencies'
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: "update-op-dependencies"
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: "update-op-dependencies"
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: "ef8f9ab8bdb22201fe1c1f954607454d5035f230"
git_commit: "793ba55aab5fa80364fa94d2936582f7ac98da0c"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "update-op-dependencies"
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 := 'update-op-dependencies'"
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 update-op-dependencies
#
# 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="2025-08-25T09:57:39Z"
LABEL org.opencontainers.image.created="2025-08-25T10:58:04Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="ef8f9ab8bdb22201fe1c1f954607454d5035f230"
LABEL org.opencontainers.image.version="v0.1.0"
LABEL org.opencontainers.image.revision="793ba55aab5fa80364fa94d2936582f7ac98da0c"
LABEL org.opencontainers.image.version="update-op-dependencies"
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 update-op-dependencies"
echo ""
echo "Creates a SpatialExperiment object from the downloaded unzipped CosMx directory"
echo "for Nanostring"
@@ -678,7 +678,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "from_cosmx_to_spatialexperiment v0.1.0"
echo "from_cosmx_to_spatialexperiment update-op-dependencies"
exit
;;
--input)
@@ -853,7 +853,7 @@ if [[ "$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:update-op-dependencies'
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: "update-op-dependencies"
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: "update-op-dependencies"
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: "ef8f9ab8bdb22201fe1c1f954607454d5035f230"
git_commit: "793ba55aab5fa80364fa94d2936582f7ac98da0c"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "update-op-dependencies"
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 := 'update-op-dependencies'"
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 update-op-dependencies
#
# 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="2025-08-25T09:57:39Z"
LABEL org.opencontainers.image.created="2025-08-25T10:58:04Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="ef8f9ab8bdb22201fe1c1f954607454d5035f230"
LABEL org.opencontainers.image.version="v0.1.0"
LABEL org.opencontainers.image.revision="793ba55aab5fa80364fa94d2936582f7ac98da0c"
LABEL org.opencontainers.image.version="update-op-dependencies"
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 update-op-dependencies"
echo ""
echo "Converts an h5mu file into a SpatialExperiment object."
echo ""
@@ -650,7 +650,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "from_h5mu_to_spatialexperiment v0.1.0"
echo "from_h5mu_to_spatialexperiment update-op-dependencies"
exit
;;
--input)
@@ -797,7 +797,7 @@ if [[ "$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:update-op-dependencies'
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: "update-op-dependencies"
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: "update-op-dependencies"
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: "ef8f9ab8bdb22201fe1c1f954607454d5035f230"
git_commit: "793ba55aab5fa80364fa94d2936582f7ac98da0c"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "update-op-dependencies"
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 := 'update-op-dependencies'"
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 update-op-dependencies
#
# 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="2025-08-25T09:57:38Z"
LABEL org.opencontainers.image.created="2025-08-25T10:58:04Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="ef8f9ab8bdb22201fe1c1f954607454d5035f230"
LABEL org.opencontainers.image.version="v0.1.0"
LABEL org.opencontainers.image.revision="793ba55aab5fa80364fa94d2936582f7ac98da0c"
LABEL org.opencontainers.image.version="update-op-dependencies"
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 update-op-dependencies"
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 [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "from_spatialdata_to_h5mu v0.1.0"
echo "from_spatialdata_to_h5mu update-op-dependencies"
exit
;;
--input)
@@ -798,7 +798,7 @@ if [[ "$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:update-op-dependencies'
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: "update-op-dependencies"
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: "update-op-dependencies"
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: "ef8f9ab8bdb22201fe1c1f954607454d5035f230"
git_commit: "793ba55aab5fa80364fa94d2936582f7ac98da0c"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "update-op-dependencies"
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 := 'update-op-dependencies'"
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 update-op-dependencies
#
# 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="2025-08-25T09:57:38Z"
LABEL org.opencontainers.image.created="2025-08-25T10:58:04Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="ef8f9ab8bdb22201fe1c1f954607454d5035f230"
LABEL org.opencontainers.image.version="v0.1.0"
LABEL org.opencontainers.image.revision="793ba55aab5fa80364fa94d2936582f7ac98da0c"
LABEL org.opencontainers.image.version="update-op-dependencies"
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 update-op-dependencies"
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 [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "from_xenium_to_h5mu v0.1.0"
echo "from_xenium_to_h5mu update-op-dependencies"
exit
;;
--input)
@@ -839,7 +839,7 @@ if [[ "$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:update-op-dependencies'
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: "update-op-dependencies"
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: "update-op-dependencies"
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: "ef8f9ab8bdb22201fe1c1f954607454d5035f230"
git_commit: "793ba55aab5fa80364fa94d2936582f7ac98da0c"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "update-op-dependencies"
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 := 'update-op-dependencies'"
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 update-op-dependencies
#
# 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="2025-08-25T09:57:39Z"
LABEL org.opencontainers.image.created="2025-08-25T10:58:05Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="ef8f9ab8bdb22201fe1c1f954607454d5035f230"
LABEL org.opencontainers.image.version="v0.1.0"
LABEL org.opencontainers.image.revision="793ba55aab5fa80364fa94d2936582f7ac98da0c"
LABEL org.opencontainers.image.version="update-op-dependencies"
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 update-op-dependencies"
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 [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "from_xenium_to_spatialdata v0.1.0"
echo "from_xenium_to_spatialdata update-op-dependencies"
exit
;;
--input)
@@ -951,7 +951,7 @@ if [[ "$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:update-op-dependencies'
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: "update-op-dependencies"
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: "update-op-dependencies"
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: "ef8f9ab8bdb22201fe1c1f954607454d5035f230"
git_commit: "793ba55aab5fa80364fa94d2936582f7ac98da0c"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "update-op-dependencies"
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 := 'update-op-dependencies'"
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 update-op-dependencies
#
# 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="2025-08-25T09:57:38Z"
LABEL org.opencontainers.image.created="2025-08-25T10:58:04Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="ef8f9ab8bdb22201fe1c1f954607454d5035f230"
LABEL org.opencontainers.image.version="v0.1.0"
LABEL org.opencontainers.image.revision="793ba55aab5fa80364fa94d2936582f7ac98da0c"
LABEL org.opencontainers.image.version="update-op-dependencies"
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 update-op-dependencies"
echo ""
echo "Creates a SpatialExperiment object from the downloaded unzipped Xenium Output"
echo "Bundle directory"
@@ -673,7 +673,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "from_xenium_to_spatialexperiment v0.1.0"
echo "from_xenium_to_spatialexperiment update-op-dependencies"
exit
;;
--input)
@@ -837,7 +837,7 @@ if [[ "$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:update-op-dependencies'
fi
# print dockerfile

10
target/executable/filter/subset_cosmx/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "subset_cosmx"
namespace: "filter"
version: "v0.1.0"
version: "update-op-dependencies"
authors:
- name: "Dorien Roosen"
roles:
@@ -191,7 +191,7 @@ engines:
id: "docker"
image: "python:3.12-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.1.0"
target_tag: "update-op-dependencies"
namespace_separator: "/"
setup:
- type: "apt"
@@ -227,11 +227,11 @@ build_info:
output: "target/executable/filter/subset_cosmx"
executable: "target/executable/filter/subset_cosmx/subset_cosmx"
viash_version: "0.9.4"
git_commit: "ef8f9ab8bdb22201fe1c1f954607454d5035f230"
git_commit: "793ba55aab5fa80364fa94d2936582f7ac98da0c"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "update-op-dependencies"
info:
test_resources:
- type: "s3"
@@ -251,7 +251,7 @@ 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 := 'update-op-dependencies'"
organization: "vsh"
links:
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

14
target/executable/filter/subset_cosmx/subset_cosmx
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# subset_cosmx v0.1.0
# subset_cosmx update-op-dependencies
#
# 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 filter subset_cosmx"
LABEL org.opencontainers.image.created="2025-08-25T09:57:38Z"
LABEL org.opencontainers.image.created="2025-08-25T10:58:03Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="ef8f9ab8bdb22201fe1c1f954607454d5035f230"
LABEL org.opencontainers.image.version="v0.1.0"
LABEL org.opencontainers.image.revision="793ba55aab5fa80364fa94d2936582f7ac98da0c"
LABEL org.opencontainers.image.version="update-op-dependencies"
VIASHDOCKER
fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "subset_cosmx v0.1.0"
echo "subset_cosmx update-op-dependencies"
echo ""
echo "Filters the output from NanoString experiment to keep only a subset of the"
echo "fields of view."
@@ -666,7 +666,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "subset_cosmx v0.1.0"
echo "subset_cosmx update-op-dependencies"
exit
;;
--input)
@@ -824,7 +824,7 @@ if [[ "$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/filter/subset_cosmx:v0.1.0'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/filter/subset_cosmx:update-op-dependencies'
fi
# print dockerfile

10
target/executable/mapping/spaceranger_count/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "spaceranger_count"
namespace: "mapping"
version: "v0.1.0"
version: "update-op-dependencies"
authors:
- name: "Jakub Majercik"
roles:
@@ -408,7 +408,7 @@ engines:
id: "docker"
image: "ghcr.io/data-intuitive/spaceranger:3.1"
target_registry: "images.viash-hub.com"
target_tag: "v0.1.0"
target_tag: "update-op-dependencies"
namespace_separator: "/"
setup:
- type: "docker"
@@ -426,11 +426,11 @@ build_info:
output: "target/executable/mapping/spaceranger_count"
executable: "target/executable/mapping/spaceranger_count/spaceranger_count"
viash_version: "0.9.4"
git_commit: "ef8f9ab8bdb22201fe1c1f954607454d5035f230"
git_commit: "793ba55aab5fa80364fa94d2936582f7ac98da0c"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "update-op-dependencies"
info:
test_resources:
- type: "s3"
@@ -450,7 +450,7 @@ 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 := 'update-op-dependencies'"
organization: "vsh"
links:
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

14
target/executable/mapping/spaceranger_count/spaceranger_count
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash
# spaceranger_count v0.1.0
# spaceranger_count update-op-dependencies
#
# 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
@@ -453,10 +453,10 @@ 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="2025-08-25T09:57:39Z"
LABEL org.opencontainers.image.created="2025-08-25T10:58:05Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial"
LABEL org.opencontainers.image.revision="ef8f9ab8bdb22201fe1c1f954607454d5035f230"
LABEL org.opencontainers.image.version="v0.1.0"
LABEL org.opencontainers.image.revision="793ba55aab5fa80364fa94d2936582f7ac98da0c"
LABEL org.opencontainers.image.version="update-op-dependencies"
VIASHDOCKER
fi
@@ -573,7 +573,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "spaceranger_count v0.1.0"
echo "spaceranger_count update-op-dependencies"
echo ""
echo "Count gene expression and protein expression reads from a single capture area."
echo ""
@@ -775,7 +775,7 @@ while [[ $# -gt 0 ]]; do
shift 1
;;
--version)
echo "spaceranger_count v0.1.0"
echo "spaceranger_count update-op-dependencies"
exit
;;
--gex_reference)
@@ -1135,7 +1135,7 @@ if [[ "$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/mapping/spaceranger_count:v0.1.0'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline_spatial/mapping/spaceranger_count:update-op-dependencies'
fi
# print dockerfile

10
target/nextflow/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: "update-op-dependencies"
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: "update-op-dependencies"
namespace_separator: "/"
setup:
- type: "apt"
@@ -290,11 +290,11 @@ 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: "ef8f9ab8bdb22201fe1c1f954607454d5035f230"
git_commit: "793ba55aab5fa80364fa94d2936582f7ac98da0c"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "update-op-dependencies"
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 := 'update-op-dependencies'"
organization: "vsh"
links:
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

14
target/nextflow/convert/from_cells2stats_to_h5mu/main.nf
View File

@@ -1,4 +1,4 @@
// from_cells2stats_to_h5mu v0.1.0
// from_cells2stats_to_h5mu update-op-dependencies
//
// 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
@@ -3035,7 +3035,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "from_cells2stats_to_h5mu",
"namespace" : "convert",
"version" : "v0.1.0",
"version" : "update-op-dependencies",
"authors" : [
{
"name" : "Dorien Roosen",
@@ -3336,7 +3336,7 @@ meta = [
"id" : "docker",
"image" : "python:3.13-slim",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.1.0",
"target_tag" : "update-op-dependencies",
"namespace_separator" : "/",
"setup" : [
{
@@ -3382,12 +3382,12 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_cells2stats_to_h5mu",
"viash_version" : "0.9.4",
"git_commit" : "ef8f9ab8bdb22201fe1c1f954607454d5035f230",
"git_commit" : "793ba55aab5fa80364fa94d2936582f7ac98da0c",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {
"name" : "openpipeline_spatial",
"version" : "v0.1.0",
"version" : "update-op-dependencies",
"info" : {
"test_resources" : [
{
@@ -3412,7 +3412,7 @@ meta = [
".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.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 := 'update-op-dependencies'"
],
"organization" : "vsh",
"links" : {
@@ -4123,7 +4123,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/openpipeline_spatial/convert/from_cells2stats_to_h5mu",
"tag" : "v0.1.0"
"tag" : "update-op-dependencies"
},
"label" : [
"lowmem",

2
target/nextflow/convert/from_cells2stats_to_h5mu/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'convert/from_cells2stats_to_h5mu'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.1.0'
version = 'update-op-dependencies'
description = 'Convert spatial data resulting from Aviti Teton sequencers that have been processed by the Element Biosciences cells2stats workflow to H5MU format.\n\nThis component processes cells2stats count matrices to create a standardized H5MU file for downstream analysis.\n\nThe component reads:\n- Parquet file containing the count matrix and metadata\n- Panel.json with target and batch information\n\nAnd outputs an H5MU file with:\n- Count data as the main .X matrix\n- Spatial coordinates in obsm\n- Cell Paint intensities in obsm (optional)\n- Nuclear count data as a layer (optional)\n- CellProfiler morphology metrics in obsm (optional)\n- Unassigned targets in obsm (optional)\n'
author = 'Dorien Roosen'
}

10
target/nextflow/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: "update-op-dependencies"
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: "update-op-dependencies"
namespace_separator: "/"
setup:
- type: "apt"
@@ -225,11 +225,11 @@ 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: "ef8f9ab8bdb22201fe1c1f954607454d5035f230"
git_commit: "793ba55aab5fa80364fa94d2936582f7ac98da0c"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "update-op-dependencies"
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 := 'update-op-dependencies'"
organization: "vsh"
links:
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

14
target/nextflow/convert/from_cosmx_to_h5mu/main.nf
View File

@@ -1,4 +1,4 @@
// from_cosmx_to_h5mu v0.1.0
// from_cosmx_to_h5mu update-op-dependencies
//
// 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
@@ -3036,7 +3036,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "from_cosmx_to_h5mu",
"namespace" : "convert",
"version" : "v0.1.0",
"version" : "update-op-dependencies",
"authors" : [
{
"name" : "Dorien Roosen",
@@ -3274,7 +3274,7 @@ meta = [
"id" : "docker",
"image" : "python:3.12-slim",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.1.0",
"target_tag" : "update-op-dependencies",
"namespace_separator" : "/",
"setup" : [
{
@@ -3331,12 +3331,12 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_h5mu",
"viash_version" : "0.9.4",
"git_commit" : "ef8f9ab8bdb22201fe1c1f954607454d5035f230",
"git_commit" : "793ba55aab5fa80364fa94d2936582f7ac98da0c",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {
"name" : "openpipeline_spatial",
"version" : "v0.1.0",
"version" : "update-op-dependencies",
"info" : {
"test_resources" : [
{
@@ -3361,7 +3361,7 @@ meta = [
".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.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 := 'update-op-dependencies'"
],
"organization" : "vsh",
"links" : {
@@ -3830,7 +3830,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/openpipeline_spatial/convert/from_cosmx_to_h5mu",
"tag" : "v0.1.0"
"tag" : "update-op-dependencies"
},
"label" : [
"lowmem",

2
target/nextflow/convert/from_cosmx_to_h5mu/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'convert/from_cosmx_to_h5mu'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.1.0'
version = 'update-op-dependencies'
description = 'Converts the output from NanoString experiment into a MuData objcet.\n - `<dataset_id>_exprMat_file.csv`: File containing the counts.\n - `<dataset_id>`_metadata_file: File containing the spatial coordinates and additional cell-level metadata.\n - `<dataset_id>_fov_file.csv`: File containing the coordinates of all the fields of view.\nIn addition to reading the regular Nanostring output, it loads CellComposite and CellLabels directories, if present,\ncontaining the images.\n'
author = 'Dorien Roosen, Weiwei Schultz'
}

10
target/nextflow/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: "update-op-dependencies"
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: "update-op-dependencies"
namespace_separator: "/"
setup:
- type: "apt"
@@ -232,11 +232,11 @@ 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: "ef8f9ab8bdb22201fe1c1f954607454d5035f230"
git_commit: "793ba55aab5fa80364fa94d2936582f7ac98da0c"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "update-op-dependencies"
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 := 'update-op-dependencies'"
organization: "vsh"
links:
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

14
target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf
View File

@@ -1,4 +1,4 @@
// from_cosmx_to_spatialexperiment v0.1.0
// from_cosmx_to_spatialexperiment update-op-dependencies
//
// 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
@@ -3035,7 +3035,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "from_cosmx_to_spatialexperiment",
"namespace" : "convert",
"version" : "v0.1.0",
"version" : "update-op-dependencies",
"authors" : [
{
"name" : "Dorien Roosen",
@@ -3280,7 +3280,7 @@ meta = [
"id" : "docker",
"image" : "rocker/r2u:24.04",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.1.0",
"target_tag" : "update-op-dependencies",
"namespace_separator" : "/",
"setup" : [
{
@@ -3322,12 +3322,12 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_spatialexperiment",
"viash_version" : "0.9.4",
"git_commit" : "ef8f9ab8bdb22201fe1c1f954607454d5035f230",
"git_commit" : "793ba55aab5fa80364fa94d2936582f7ac98da0c",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {
"name" : "openpipeline_spatial",
"version" : "v0.1.0",
"version" : "update-op-dependencies",
"info" : {
"test_resources" : [
{
@@ -3352,7 +3352,7 @@ meta = [
".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.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 := 'update-op-dependencies'"
],
"organization" : "vsh",
"links" : {
@@ -3821,7 +3821,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/openpipeline_spatial/convert/from_cosmx_to_spatialexperiment",
"tag" : "v0.1.0"
"tag" : "update-op-dependencies"
},
"label" : [
"lowmem",

2
target/nextflow/convert/from_cosmx_to_spatialexperiment/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'convert/from_cosmx_to_spatialexperiment'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.1.0'
version = 'update-op-dependencies'
description = 'Creates a SpatialExperiment object from the downloaded unzipped CosMx directory for Nanostring\nCosMx spatial gene expression data, and saves it as a SpatialExperiment object.\nThe constructor assumes the downloaded unzipped CosMx Folder has the following structure:\n\nMandatory files\n· | — *_exprMat_file.csv\n· | — *_metadata_file.csv\nOptional files, by default added to the metadata() as a list of paths (will be converted to parquet):\n· | —*_fov_positions_file.csv\n· | — *_tx_file.csv\n· | — *_polygons.csv\n'
author = 'Dorien Roosen'
}

10
target/nextflow/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: "update-op-dependencies"
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: "update-op-dependencies"
namespace_separator: "/"
setup:
- type: "apt"
@@ -224,11 +224,11 @@ 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: "ef8f9ab8bdb22201fe1c1f954607454d5035f230"
git_commit: "793ba55aab5fa80364fa94d2936582f7ac98da0c"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "update-op-dependencies"
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 := 'update-op-dependencies'"
organization: "vsh"
links:
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

14
target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf
View File

@@ -1,4 +1,4 @@
// from_h5mu_to_spatialexperiment v0.1.0
// from_h5mu_to_spatialexperiment update-op-dependencies
//
// 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
@@ -3035,7 +3035,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "from_h5mu_to_spatialexperiment",
"namespace" : "convert",
"version" : "v0.1.0",
"version" : "update-op-dependencies",
"authors" : [
{
"name" : "Dorien Roosen",
@@ -3257,7 +3257,7 @@ meta = [
"id" : "docker",
"image" : "rocker/r2u:22.04",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.1.0",
"target_tag" : "update-op-dependencies",
"namespace_separator" : "/",
"setup" : [
{
@@ -3332,12 +3332,12 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_h5mu_to_spatialexperiment",
"viash_version" : "0.9.4",
"git_commit" : "ef8f9ab8bdb22201fe1c1f954607454d5035f230",
"git_commit" : "793ba55aab5fa80364fa94d2936582f7ac98da0c",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {
"name" : "openpipeline_spatial",
"version" : "v0.1.0",
"version" : "update-op-dependencies",
"info" : {
"test_resources" : [
{
@@ -3362,7 +3362,7 @@ meta = [
".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.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 := 'update-op-dependencies'"
],
"organization" : "vsh",
"links" : {
@@ -3910,7 +3910,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/openpipeline_spatial/convert/from_h5mu_to_spatialexperiment",
"tag" : "v0.1.0"
"tag" : "update-op-dependencies"
},
"label" : [
"lowmem",

2
target/nextflow/convert/from_h5mu_to_spatialexperiment/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'convert/from_h5mu_to_spatialexperiment'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.1.0'
version = 'update-op-dependencies'
description = 'Converts an h5mu file into a SpatialExperiment object.\n'
author = 'Dorien Roosen'
}

10
target/nextflow/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: "update-op-dependencies"
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: "update-op-dependencies"
namespace_separator: "/"
setup:
- type: "apt"
@@ -220,11 +220,11 @@ 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: "ef8f9ab8bdb22201fe1c1f954607454d5035f230"
git_commit: "793ba55aab5fa80364fa94d2936582f7ac98da0c"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "update-op-dependencies"
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 := 'update-op-dependencies'"
organization: "vsh"
links:
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

14
target/nextflow/convert/from_spatialdata_to_h5mu/main.nf
View File

@@ -1,4 +1,4 @@
// from_spatialdata_to_h5mu v0.1.0
// from_spatialdata_to_h5mu update-op-dependencies
//
// 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
@@ -3036,7 +3036,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "from_spatialdata_to_h5mu",
"namespace" : "convert",
"version" : "v0.1.0",
"version" : "update-op-dependencies",
"authors" : [
{
"name" : "Dorien Roosen",
@@ -3274,7 +3274,7 @@ meta = [
"id" : "docker",
"image" : "python:3.12-slim",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.1.0",
"target_tag" : "update-op-dependencies",
"namespace_separator" : "/",
"setup" : [
{
@@ -3330,12 +3330,12 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_spatialdata_to_h5mu",
"viash_version" : "0.9.4",
"git_commit" : "ef8f9ab8bdb22201fe1c1f954607454d5035f230",
"git_commit" : "793ba55aab5fa80364fa94d2936582f7ac98da0c",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {
"name" : "openpipeline_spatial",
"version" : "v0.1.0",
"version" : "update-op-dependencies",
"info" : {
"test_resources" : [
{
@@ -3360,7 +3360,7 @@ meta = [
".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.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 := 'update-op-dependencies'"
],
"organization" : "vsh",
"links" : {
@@ -3814,7 +3814,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/openpipeline_spatial/convert/from_spatialdata_to_h5mu",
"tag" : "v0.1.0"
"tag" : "update-op-dependencies"
},
"label" : [
"lowmem",

2
target/nextflow/convert/from_spatialdata_to_h5mu/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'convert/from_spatialdata_to_h5mu'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.1.0'
version = 'update-op-dependencies'
description = 'Reads in the Tables field stored in a SpatialData object and converts it to an h5mu file.\n \n'
author = 'Dorien Roosen, Weiwei Schultz'
}

10
target/nextflow/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: "update-op-dependencies"
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: "update-op-dependencies"
namespace_separator: "/"
setup:
- type: "apt"
@@ -233,11 +233,11 @@ 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: "ef8f9ab8bdb22201fe1c1f954607454d5035f230"
git_commit: "793ba55aab5fa80364fa94d2936582f7ac98da0c"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "update-op-dependencies"
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 := 'update-op-dependencies'"
organization: "vsh"
links:
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

14
target/nextflow/convert/from_xenium_to_h5mu/main.nf
View File

@@ -1,4 +1,4 @@
// from_xenium_to_h5mu v0.1.0
// from_xenium_to_h5mu update-op-dependencies
//
// 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
@@ -3035,7 +3035,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "from_xenium_to_h5mu",
"namespace" : "convert",
"version" : "v0.1.0",
"version" : "update-op-dependencies",
"authors" : [
{
"name" : "Dorien Roosen",
@@ -3284,7 +3284,7 @@ meta = [
"id" : "docker",
"image" : "python:3.12-slim",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.1.0",
"target_tag" : "update-op-dependencies",
"namespace_separator" : "/",
"setup" : [
{
@@ -3331,12 +3331,12 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_h5mu",
"viash_version" : "0.9.4",
"git_commit" : "ef8f9ab8bdb22201fe1c1f954607454d5035f230",
"git_commit" : "793ba55aab5fa80364fa94d2936582f7ac98da0c",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {
"name" : "openpipeline_spatial",
"version" : "v0.1.0",
"version" : "update-op-dependencies",
"info" : {
"test_resources" : [
{
@@ -3361,7 +3361,7 @@ meta = [
".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.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 := 'update-op-dependencies'"
],
"organization" : "vsh",
"links" : {
@@ -3862,7 +3862,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/openpipeline_spatial/convert/from_xenium_to_h5mu",
"tag" : "v0.1.0"
"tag" : "update-op-dependencies"
},
"label" : [
"lowmem",

2
target/nextflow/convert/from_xenium_to_h5mu/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'convert/from_xenium_to_h5mu'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.1.0'
version = 'update-op-dependencies'
description = 'Converts the output from Xenium to a single .h5mu file, where the count matrix is written to the `rna` modality.\nThe following files are expected to be present in the Xenium output bundle:\n├── cell_feature_matrix.h5\n├── cells.parquet\n├── experiment.xenium\n└── metrics_summary.csv\n'
author = 'Dorien Roosen'
}

10
target/nextflow/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: "update-op-dependencies"
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: "update-op-dependencies"
namespace_separator: "/"
setup:
- type: "apt"
@@ -314,11 +314,11 @@ 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: "ef8f9ab8bdb22201fe1c1f954607454d5035f230"
git_commit: "793ba55aab5fa80364fa94d2936582f7ac98da0c"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "update-op-dependencies"
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 := 'update-op-dependencies'"
organization: "vsh"
links:
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

14
target/nextflow/convert/from_xenium_to_spatialdata/main.nf
View File

@@ -1,4 +1,4 @@
// from_xenium_to_spatialdata v0.1.0
// from_xenium_to_spatialdata update-op-dependencies
//
// 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
@@ -3036,7 +3036,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "from_xenium_to_spatialdata",
"namespace" : "convert",
"version" : "v0.1.0",
"version" : "update-op-dependencies",
"authors" : [
{
"name" : "Dorien Roosen",
@@ -3373,7 +3373,7 @@ meta = [
"id" : "docker",
"image" : "python:3.12-slim",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.1.0",
"target_tag" : "update-op-dependencies",
"namespace_separator" : "/",
"setup" : [
{
@@ -3425,12 +3425,12 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialdata",
"viash_version" : "0.9.4",
"git_commit" : "ef8f9ab8bdb22201fe1c1f954607454d5035f230",
"git_commit" : "793ba55aab5fa80364fa94d2936582f7ac98da0c",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {
"name" : "openpipeline_spatial",
"version" : "v0.1.0",
"version" : "update-op-dependencies",
"info" : {
"test_resources" : [
{
@@ -3455,7 +3455,7 @@ meta = [
".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.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 := 'update-op-dependencies'"
],
"organization" : "vsh",
"links" : {
@@ -3927,7 +3927,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/openpipeline_spatial/convert/from_xenium_to_spatialdata",
"tag" : "v0.1.0"
"tag" : "update-op-dependencies"
},
"label" : [
"lowmem",

2
target/nextflow/convert/from_xenium_to_spatialdata/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'convert/from_xenium_to_spatialdata'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.1.0'
version = 'update-op-dependencies'
description = 'Converts the output from 10X Genomics Xenium dataset into a SpatialData objcet.\nBy default, the following files will be converted:\n - `experiment.xenium`: File containing specifications.\n - `nucleus_boundaries.parquet`: Polygons of nucleus boundaries.\n - `cell_boundaries.parquet`: Polygons of cell boundaries.\n - `transcripts.parquet`: File containing transcripts.\n - `cell_feature_matrix.h5`: File containing cell feature matrix.\n - `cells.parquet`: File containing cell metadata.\n - `morphology_mip.ome.tif`: File containing morphology mip.\n - `morphology_focus.ome.tif`: File containing morphology focus.\n \n'
author = 'Dorien Roosen, Weiwei Schultz'
}

10
target/nextflow/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: "update-op-dependencies"
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: "update-op-dependencies"
namespace_separator: "/"
setup:
- type: "apt"
@@ -222,11 +222,11 @@ 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: "ef8f9ab8bdb22201fe1c1f954607454d5035f230"
git_commit: "793ba55aab5fa80364fa94d2936582f7ac98da0c"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "update-op-dependencies"
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 := 'update-op-dependencies'"
organization: "vsh"
links:
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

14
target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf
View File

@@ -1,4 +1,4 @@
// from_xenium_to_spatialexperiment v0.1.0
// from_xenium_to_spatialexperiment update-op-dependencies
//
// 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
@@ -3035,7 +3035,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "from_xenium_to_spatialexperiment",
"namespace" : "convert",
"version" : "v0.1.0",
"version" : "update-op-dependencies",
"authors" : [
{
"name" : "Dorien Roosen",
@@ -3269,7 +3269,7 @@ meta = [
"id" : "docker",
"image" : "rocker/r2u:24.04",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.1.0",
"target_tag" : "update-op-dependencies",
"namespace_separator" : "/",
"setup" : [
{
@@ -3311,12 +3311,12 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialexperiment",
"viash_version" : "0.9.4",
"git_commit" : "ef8f9ab8bdb22201fe1c1f954607454d5035f230",
"git_commit" : "793ba55aab5fa80364fa94d2936582f7ac98da0c",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {
"name" : "openpipeline_spatial",
"version" : "v0.1.0",
"version" : "update-op-dependencies",
"info" : {
"test_resources" : [
{
@@ -3341,7 +3341,7 @@ meta = [
".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.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 := 'update-op-dependencies'"
],
"organization" : "vsh",
"links" : {
@@ -3801,7 +3801,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/openpipeline_spatial/convert/from_xenium_to_spatialexperiment",
"tag" : "v0.1.0"
"tag" : "update-op-dependencies"
},
"label" : [
"lowmem",

2
target/nextflow/convert/from_xenium_to_spatialexperiment/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'convert/from_xenium_to_spatialexperiment'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.1.0'
version = 'update-op-dependencies'
description = 'Creates a SpatialExperiment object from the downloaded unzipped Xenium Output Bundle directory\nfor 10x Genomics Xenium spatial gene expression data, and saves it as a SpatialExperiment object.\nThe constructor assumes the downloaded unzipped Xenium Output Bundle has the following structure:\n\nMandatory files\n· | — cell_feature_matrix.h5\n· | — cells.parquet\nOptional files, by default added to the metadata() as a list of paths (will be converted to parquet):\n· | — transcripts.parquet\n· | — cell_boundaries.parquet\n· | — nucleus_boundaries.parquet\n· | — experiment.xenium\n'
author = 'Dorien Roosen'
}

10
target/nextflow/filter/subset_cosmx/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "subset_cosmx"
namespace: "filter"
version: "v0.1.0"
version: "update-op-dependencies"
authors:
- name: "Dorien Roosen"
roles:
@@ -191,7 +191,7 @@ engines:
id: "docker"
image: "python:3.12-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.1.0"
target_tag: "update-op-dependencies"
namespace_separator: "/"
setup:
- type: "apt"
@@ -227,11 +227,11 @@ build_info:
output: "target/nextflow/filter/subset_cosmx"
executable: "target/nextflow/filter/subset_cosmx/main.nf"
viash_version: "0.9.4"
git_commit: "ef8f9ab8bdb22201fe1c1f954607454d5035f230"
git_commit: "793ba55aab5fa80364fa94d2936582f7ac98da0c"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "update-op-dependencies"
info:
test_resources:
- type: "s3"
@@ -251,7 +251,7 @@ 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 := 'update-op-dependencies'"
organization: "vsh"
links:
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

14
target/nextflow/filter/subset_cosmx/main.nf
View File

@@ -1,4 +1,4 @@
// subset_cosmx v0.1.0
// subset_cosmx update-op-dependencies
//
// 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
@@ -3036,7 +3036,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "subset_cosmx",
"namespace" : "filter",
"version" : "v0.1.0",
"version" : "update-op-dependencies",
"authors" : [
{
"name" : "Dorien Roosen",
@@ -3281,7 +3281,7 @@ meta = [
"id" : "docker",
"image" : "python:3.12-slim",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.1.0",
"target_tag" : "update-op-dependencies",
"namespace_separator" : "/",
"setup" : [
{
@@ -3333,12 +3333,12 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/filter/subset_cosmx",
"viash_version" : "0.9.4",
"git_commit" : "ef8f9ab8bdb22201fe1c1f954607454d5035f230",
"git_commit" : "793ba55aab5fa80364fa94d2936582f7ac98da0c",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {
"name" : "openpipeline_spatial",
"version" : "v0.1.0",
"version" : "update-op-dependencies",
"info" : {
"test_resources" : [
{
@@ -3363,7 +3363,7 @@ meta = [
".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.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 := 'update-op-dependencies'"
],
"organization" : "vsh",
"links" : {
@@ -3858,7 +3858,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/openpipeline_spatial/filter/subset_cosmx",
"tag" : "v0.1.0"
"tag" : "update-op-dependencies"
},
"label" : [
"lowmem",

2
target/nextflow/filter/subset_cosmx/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'filter/subset_cosmx'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.1.0'
version = 'update-op-dependencies'
description = 'Filters the output from NanoString experiment to keep only a subset of the fields of view.\nExpected input folder structure:\npath/to/dataset/\n ├── CellComposite/\n ├── CellLabels/\n ├── CellOverlay/\n ├── CompartmentLabels/\n ├── <dataset_id>_exprMat_file.csv\n ├── <dataset_id>_fov_positions_file.csv\n ├── <dataset_id>_metadata_file.csv\n └── <dataset_id>_tx_file.csv \n'
author = 'Dorien Roosen, Weiwei Schultz'
}

10
target/nextflow/mapping/spaceranger_count/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "spaceranger_count"
namespace: "mapping"
version: "v0.1.0"
version: "update-op-dependencies"
authors:
- name: "Jakub Majercik"
roles:
@@ -408,7 +408,7 @@ engines:
id: "docker"
image: "ghcr.io/data-intuitive/spaceranger:3.1"
target_registry: "images.viash-hub.com"
target_tag: "v0.1.0"
target_tag: "update-op-dependencies"
namespace_separator: "/"
setup:
- type: "docker"
@@ -426,11 +426,11 @@ build_info:
output: "target/nextflow/mapping/spaceranger_count"
executable: "target/nextflow/mapping/spaceranger_count/main.nf"
viash_version: "0.9.4"
git_commit: "ef8f9ab8bdb22201fe1c1f954607454d5035f230"
git_commit: "793ba55aab5fa80364fa94d2936582f7ac98da0c"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "update-op-dependencies"
info:
test_resources:
- type: "s3"
@@ -450,7 +450,7 @@ 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 := 'update-op-dependencies'"
organization: "vsh"
links:
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

14
target/nextflow/mapping/spaceranger_count/main.nf
View File

@@ -1,4 +1,4 @@
// spaceranger_count v0.1.0
// spaceranger_count update-op-dependencies
//
// 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
@@ -3035,7 +3035,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "spaceranger_count",
"namespace" : "mapping",
"version" : "v0.1.0",
"version" : "update-op-dependencies",
"authors" : [
{
"name" : "Jakub Majercik",
@@ -3526,7 +3526,7 @@ meta = [
"id" : "docker",
"image" : "ghcr.io/data-intuitive/spaceranger:3.1",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.1.0",
"target_tag" : "update-op-dependencies",
"namespace_separator" : "/",
"setup" : [
{
@@ -3548,12 +3548,12 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/mapping/spaceranger_count",
"viash_version" : "0.9.4",
"git_commit" : "ef8f9ab8bdb22201fe1c1f954607454d5035f230",
"git_commit" : "793ba55aab5fa80364fa94d2936582f7ac98da0c",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {
"name" : "openpipeline_spatial",
"version" : "v0.1.0",
"version" : "update-op-dependencies",
"info" : {
"test_resources" : [
{
@@ -3578,7 +3578,7 @@ meta = [
".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.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 := 'update-op-dependencies'"
],
"organization" : "vsh",
"links" : {
@@ -4072,7 +4072,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/openpipeline_spatial/mapping/spaceranger_count",
"tag" : "v0.1.0"
"tag" : "update-op-dependencies"
},
"tag" : "$id"
}'''),

2
target/nextflow/mapping/spaceranger_count/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'mapping/spaceranger_count'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.1.0'
version = 'update-op-dependencies'
description = 'Count gene expression and protein expression reads from a single capture area.'
author = 'Jakub Majercik'
}

8
target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "spatial_process_samples"
namespace: "workflows/multiomics"
version: "v0.1.0"
version: "update-op-dependencies"
authors:
- name: "Dries Schaumont"
roles:
@@ -640,13 +640,13 @@ 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: "ef8f9ab8bdb22201fe1c1f954607454d5035f230"
git_commit: "793ba55aab5fa80364fa94d2936582f7ac98da0c"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
dependencies:
- "target/dependencies/vsh/vsh/openpipeline/v3.0.0/nextflow/workflows/multiomics/process_samples"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "update-op-dependencies"
info:
test_resources:
- type: "s3"
@@ -666,7 +666,7 @@ 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 := 'update-op-dependencies'"
organization: "vsh"
links:
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

10
target/nextflow/workflows/multiomics/spatial_process_samples/main.nf
View File

@@ -1,4 +1,4 @@
// spatial_process_samples v0.1.0
// spatial_process_samples update-op-dependencies
//
// 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
@@ -3037,7 +3037,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "spatial_process_samples",
"namespace" : "workflows/multiomics",
"version" : "v0.1.0",
"version" : "update-op-dependencies",
"authors" : [
{
"name" : "Dries Schaumont",
@@ -3807,12 +3807,12 @@ meta = [
"engine" : "native",
"output" : "/workdir/root/repo/target/nextflow/workflows/multiomics/spatial_process_samples",
"viash_version" : "0.9.4",
"git_commit" : "ef8f9ab8bdb22201fe1c1f954607454d5035f230",
"git_commit" : "793ba55aab5fa80364fa94d2936582f7ac98da0c",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {
"name" : "openpipeline_spatial",
"version" : "v0.1.0",
"version" : "update-op-dependencies",
"info" : {
"test_resources" : [
{
@@ -3837,7 +3837,7 @@ meta = [
".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.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 := 'update-op-dependencies'"
],
"organization" : "vsh",
"links" : {

2
target/nextflow/workflows/multiomics/spatial_process_samples/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'workflows/multiomics/spatial_process_samples'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.1.0'
version = 'update-op-dependencies'
description = 'A pipeline to pre-process multiple spatial omics samples.'
author = 'Dries Schaumont, Dorien Roosen, Weiwei Schultz'
}

8
target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "spatial_qc"
namespace: "workflows/qc"
version: "v0.1.0"
version: "update-op-dependencies"
authors:
- name: "Dries Schaumont"
roles:
@@ -387,13 +387,13 @@ 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: "ef8f9ab8bdb22201fe1c1f954607454d5035f230"
git_commit: "793ba55aab5fa80364fa94d2936582f7ac98da0c"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
dependencies:
- "target/dependencies/vsh/vsh/openpipeline/v3.0.0/nextflow/workflows/qc/qc"
package_config:
name: "openpipeline_spatial"
version: "v0.1.0"
version: "update-op-dependencies"
info:
test_resources:
- type: "s3"
@@ -413,7 +413,7 @@ 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 := 'update-op-dependencies'"
organization: "vsh"
links:
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"

10
target/nextflow/workflows/qc/spatial_qc/main.nf
View File

@@ -1,4 +1,4 @@
// spatial_qc v0.1.0
// spatial_qc update-op-dependencies
//
// 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
@@ -3037,7 +3037,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "spatial_qc",
"namespace" : "workflows/qc",
"version" : "v0.1.0",
"version" : "update-op-dependencies",
"authors" : [
{
"name" : "Dries Schaumont",
@@ -3505,12 +3505,12 @@ meta = [
"engine" : "native",
"output" : "/workdir/root/repo/target/nextflow/workflows/qc/spatial_qc",
"viash_version" : "0.9.4",
"git_commit" : "ef8f9ab8bdb22201fe1c1f954607454d5035f230",
"git_commit" : "793ba55aab5fa80364fa94d2936582f7ac98da0c",
"git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial"
},
"package_config" : {
"name" : "openpipeline_spatial",
"version" : "v0.1.0",
"version" : "update-op-dependencies",
"info" : {
"test_resources" : [
{
@@ -3535,7 +3535,7 @@ meta = [
".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.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 := 'update-op-dependencies'"
],
"organization" : "vsh",
"links" : {

2
target/nextflow/workflows/qc/spatial_qc/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'workflows/qc/spatial_qc'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.1.0'
version = 'update-op-dependencies'
description = 'A pipeline to add basic qc statistics to a MuData containing spatial data.'
author = 'Dries Schaumont, Dorien Roosen, Weiwei Schultz'
}