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

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

Source commit: 793ba55aab

Source message: cleanup

CHANGELOG.md

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

_viash.yaml

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

target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml

@@ -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"

target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu

@@ -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.revision="793ba55aab5fa80364fa94d2936582f7ac98da0c"
-LABEL org.opencontainers.image.version="v0.1.0"
+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

target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml

@@ -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"

target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu

@@ -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.revision="793ba55aab5fa80364fa94d2936582f7ac98da0c"
-LABEL org.opencontainers.image.version="v0.1.0"
+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

target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml

@@ -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"

target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment

@@ -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.revision="793ba55aab5fa80364fa94d2936582f7ac98da0c"
-LABEL org.opencontainers.image.version="v0.1.0"
+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

target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml

@@ -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"

target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment

@@ -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.revision="793ba55aab5fa80364fa94d2936582f7ac98da0c"
-LABEL org.opencontainers.image.version="v0.1.0"
+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

target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml

@@ -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"

target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu

@@ -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.revision="793ba55aab5fa80364fa94d2936582f7ac98da0c"
-LABEL org.opencontainers.image.version="v0.1.0"
+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

target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml

@@ -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"

target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu

@@ -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.revision="793ba55aab5fa80364fa94d2936582f7ac98da0c"
-LABEL org.opencontainers.image.version="v0.1.0"
+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

target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml

@@ -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"

target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata

@@ -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.revision="793ba55aab5fa80364fa94d2936582f7ac98da0c"
-LABEL org.opencontainers.image.version="v0.1.0"
+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

target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml

@@ -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"

target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment

@@ -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.revision="793ba55aab5fa80364fa94d2936582f7ac98da0c"
-LABEL org.opencontainers.image.version="v0.1.0"
+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

target/executable/filter/subset_cosmx/.config.vsh.yaml

@@ -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"

target/executable/filter/subset_cosmx/subset_cosmx

@@ -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.revision="793ba55aab5fa80364fa94d2936582f7ac98da0c"
-LABEL org.opencontainers.image.version="v0.1.0"
+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

target/executable/mapping/spaceranger_count/.config.vsh.yaml

@@ -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"

target/executable/mapping/spaceranger_count/spaceranger_count

@@ -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.revision="793ba55aab5fa80364fa94d2936582f7ac98da0c"
-LABEL org.opencontainers.image.version="v0.1.0"
+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

target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml

@@ -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"

target/nextflow/convert/from_cells2stats_to_h5mu/main.nf

@@ -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",

target/nextflow/convert/from_cells2stats_to_h5mu/nextflow.config

@@ -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'
 }

target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml

@@ -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"

target/nextflow/convert/from_cosmx_to_h5mu/main.nf

@@ -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",

target/nextflow/convert/from_cosmx_to_h5mu/nextflow.config

@@ -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'
 }

target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml

@@ -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"

target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf

@@ -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",

target/nextflow/convert/from_cosmx_to_spatialexperiment/nextflow.config

@@ -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'
 }

target/nextflow/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml

@@ -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"

target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf

@@ -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",

target/nextflow/convert/from_h5mu_to_spatialexperiment/nextflow.config

@@ -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'
 }

target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml

@@ -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"

target/nextflow/convert/from_spatialdata_to_h5mu/main.nf

@@ -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",

target/nextflow/convert/from_spatialdata_to_h5mu/nextflow.config

@@ -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'
 }

target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml

@@ -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"

target/nextflow/convert/from_xenium_to_h5mu/main.nf

@@ -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",

target/nextflow/convert/from_xenium_to_h5mu/nextflow.config

@@ -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'
 }

target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml

@@ -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"

target/nextflow/convert/from_xenium_to_spatialdata/main.nf

@@ -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",

target/nextflow/convert/from_xenium_to_spatialdata/nextflow.config

@@ -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'
 }

target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml

@@ -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"

target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf

@@ -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",

target/nextflow/convert/from_xenium_to_spatialexperiment/nextflow.config

@@ -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'
 }

target/nextflow/filter/subset_cosmx/.config.vsh.yaml

@@ -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"

target/nextflow/filter/subset_cosmx/main.nf

@@ -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",

target/nextflow/filter/subset_cosmx/nextflow.config

@@ -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'
 }

target/nextflow/mapping/spaceranger_count/.config.vsh.yaml

@@ -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"

target/nextflow/mapping/spaceranger_count/main.nf

@@ -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"
 }'''),

target/nextflow/mapping/spaceranger_count/nextflow.config

@@ -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'
 }

target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml

@@ -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"

target/nextflow/workflows/multiomics/spatial_process_samples/main.nf

@@ -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" : {

target/nextflow/workflows/multiomics/spatial_process_samples/nextflow.config

@@ -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'
 }

target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml

@@ -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"

target/nextflow/workflows/qc/spatial_qc/main.nf

@@ -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" : {

target/nextflow/workflows/qc/spatial_qc/nextflow.config

@@ -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'
 }