diff --git a/CHANGELOG.md b/CHANGELOG.md index 9a4468f..5bf9cb3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,4 +1,4 @@ -# openpipeline_spatial 0.1.0 +# openpipeline_spatial 0.0.0 ## NEW FUNCTIONALITY diff --git a/_viash.yaml b/_viash.yaml index 884cccf..504fcce 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,4 +1,3 @@ -version: v0.1.0 viash_version: 0.9.4 source: src diff --git a/target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml index 683a483..d790f94 100644 --- a/target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml +++ b/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" diff --git a/target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu b/target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu index 59def9b..e06c874 100755 --- a/target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu +++ b/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.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 diff --git a/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml index 8666600..df972e7 100644 --- a/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml +++ b/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" diff --git a/target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu b/target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu index 3e6ca6b..89653a7 100755 --- a/target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu +++ b/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.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 " - \`_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 diff --git a/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml b/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml index f18ab58..b5a5ee7 100644 --- a/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml +++ b/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" diff --git a/target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment b/target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment index 3490d61..1d95912 100755 --- a/target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment +++ b/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.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 diff --git a/target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml b/target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml index 2ebabdc..bd77f2a 100644 --- a/target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml +++ b/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" diff --git a/target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment b/target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment index a262aee..6765941 100755 --- a/target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment +++ b/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.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 diff --git a/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml index 294c17a..91f9344 100644 --- a/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml +++ b/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" diff --git a/target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu b/target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu index c74598b..6d161f2 100755 --- a/target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu +++ b/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.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 diff --git a/target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml index 2f912e2..04808a5 100644 --- a/target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml +++ b/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" diff --git a/target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu b/target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu index 566e291..1ca6eec 100755 --- a/target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu +++ b/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.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 diff --git a/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml b/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml index 48392d0..4c16590 100644 --- a/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml +++ b/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" diff --git a/target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata b/target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata index 0fdc8ba..d2296aa 100755 --- a/target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata +++ b/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.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 diff --git a/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml b/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml index 4f2d4ab..fdf8cee 100644 --- a/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml +++ b/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" diff --git a/target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment b/target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment index 9b1014b..50f5657 100755 --- a/target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment +++ b/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.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 diff --git a/target/executable/filter/subset_cosmx/.config.vsh.yaml b/target/executable/filter/subset_cosmx/.config.vsh.yaml index e16536c..06ba0a0 100644 --- a/target/executable/filter/subset_cosmx/.config.vsh.yaml +++ b/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" diff --git a/target/executable/filter/subset_cosmx/subset_cosmx b/target/executable/filter/subset_cosmx/subset_cosmx index 1f35b69..5ea0a04 100755 --- a/target/executable/filter/subset_cosmx/subset_cosmx +++ b/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.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 diff --git a/target/executable/mapping/spaceranger_count/.config.vsh.yaml b/target/executable/mapping/spaceranger_count/.config.vsh.yaml index 474e919..f1209c6 100644 --- a/target/executable/mapping/spaceranger_count/.config.vsh.yaml +++ b/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" diff --git a/target/executable/mapping/spaceranger_count/spaceranger_count b/target/executable/mapping/spaceranger_count/spaceranger_count index e10c45a..f9206bd 100755 --- a/target/executable/mapping/spaceranger_count/spaceranger_count +++ b/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.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 diff --git a/target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml index ddc9b85..e609a95 100644 --- a/target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml +++ b/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" diff --git a/target/nextflow/convert/from_cells2stats_to_h5mu/main.nf b/target/nextflow/convert/from_cells2stats_to_h5mu/main.nf index e6efb06..4bff44c 100644 --- a/target/nextflow/convert/from_cells2stats_to_h5mu/main.nf +++ b/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", diff --git a/target/nextflow/convert/from_cells2stats_to_h5mu/nextflow.config b/target/nextflow/convert/from_cells2stats_to_h5mu/nextflow.config index 98b884f..da1a461 100644 --- a/target/nextflow/convert/from_cells2stats_to_h5mu/nextflow.config +++ b/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' } diff --git a/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml index 62d6769..3282cf1 100644 --- a/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml +++ b/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" diff --git a/target/nextflow/convert/from_cosmx_to_h5mu/main.nf b/target/nextflow/convert/from_cosmx_to_h5mu/main.nf index 6e23ccf..7ee795a 100644 --- a/target/nextflow/convert/from_cosmx_to_h5mu/main.nf +++ b/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", diff --git a/target/nextflow/convert/from_cosmx_to_h5mu/nextflow.config b/target/nextflow/convert/from_cosmx_to_h5mu/nextflow.config index 6148394..73fc182 100644 --- a/target/nextflow/convert/from_cosmx_to_h5mu/nextflow.config +++ b/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 - `_exprMat_file.csv`: File containing the counts.\n - ``_metadata_file: File containing the spatial coordinates and additional cell-level metadata.\n - `_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' } diff --git a/target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml b/target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml index 2884091..91dd1a4 100644 --- a/target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml +++ b/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" diff --git a/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf b/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf index 0b1d033..c0b1df1 100644 --- a/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf +++ b/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", diff --git a/target/nextflow/convert/from_cosmx_to_spatialexperiment/nextflow.config b/target/nextflow/convert/from_cosmx_to_spatialexperiment/nextflow.config index fd28d4a..f01e571 100644 --- a/target/nextflow/convert/from_cosmx_to_spatialexperiment/nextflow.config +++ b/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' } diff --git a/target/nextflow/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml b/target/nextflow/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml index 01198ce..409c7ee 100644 --- a/target/nextflow/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml +++ b/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" diff --git a/target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf b/target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf index 35f1a48..cf87e42 100644 --- a/target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf +++ b/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", diff --git a/target/nextflow/convert/from_h5mu_to_spatialexperiment/nextflow.config b/target/nextflow/convert/from_h5mu_to_spatialexperiment/nextflow.config index d87780a..bde4404 100644 --- a/target/nextflow/convert/from_h5mu_to_spatialexperiment/nextflow.config +++ b/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' } diff --git a/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml index 2ebf73f..5e93d25 100644 --- a/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml +++ b/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" diff --git a/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf b/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf index ccfc17e..b6eca53 100644 --- a/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf +++ b/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", diff --git a/target/nextflow/convert/from_spatialdata_to_h5mu/nextflow.config b/target/nextflow/convert/from_spatialdata_to_h5mu/nextflow.config index c723588..d42b30d 100644 --- a/target/nextflow/convert/from_spatialdata_to_h5mu/nextflow.config +++ b/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' } diff --git a/target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml index b8bd6bd..5983c23 100644 --- a/target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml +++ b/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" diff --git a/target/nextflow/convert/from_xenium_to_h5mu/main.nf b/target/nextflow/convert/from_xenium_to_h5mu/main.nf index bfc1f66..c37e4cc 100644 --- a/target/nextflow/convert/from_xenium_to_h5mu/main.nf +++ b/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", diff --git a/target/nextflow/convert/from_xenium_to_h5mu/nextflow.config b/target/nextflow/convert/from_xenium_to_h5mu/nextflow.config index 83579b7..2f8427d 100644 --- a/target/nextflow/convert/from_xenium_to_h5mu/nextflow.config +++ b/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' } diff --git a/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml b/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml index e3fe043..1894cce 100644 --- a/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml +++ b/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" diff --git a/target/nextflow/convert/from_xenium_to_spatialdata/main.nf b/target/nextflow/convert/from_xenium_to_spatialdata/main.nf index c466299..41f2af5 100644 --- a/target/nextflow/convert/from_xenium_to_spatialdata/main.nf +++ b/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", diff --git a/target/nextflow/convert/from_xenium_to_spatialdata/nextflow.config b/target/nextflow/convert/from_xenium_to_spatialdata/nextflow.config index 50dd1c2..ce835a0 100644 --- a/target/nextflow/convert/from_xenium_to_spatialdata/nextflow.config +++ b/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' } diff --git a/target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml b/target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml index 7edf78a..3a5bc3b 100644 --- a/target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml +++ b/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" diff --git a/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf b/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf index f1a4c7b..fea6007 100644 --- a/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf +++ b/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", diff --git a/target/nextflow/convert/from_xenium_to_spatialexperiment/nextflow.config b/target/nextflow/convert/from_xenium_to_spatialexperiment/nextflow.config index 9a71841..95a9fb3 100644 --- a/target/nextflow/convert/from_xenium_to_spatialexperiment/nextflow.config +++ b/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' } diff --git a/target/nextflow/filter/subset_cosmx/.config.vsh.yaml b/target/nextflow/filter/subset_cosmx/.config.vsh.yaml index e255810..9f26c96 100644 --- a/target/nextflow/filter/subset_cosmx/.config.vsh.yaml +++ b/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" diff --git a/target/nextflow/filter/subset_cosmx/main.nf b/target/nextflow/filter/subset_cosmx/main.nf index 84d5963..d9dd8df 100644 --- a/target/nextflow/filter/subset_cosmx/main.nf +++ b/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", diff --git a/target/nextflow/filter/subset_cosmx/nextflow.config b/target/nextflow/filter/subset_cosmx/nextflow.config index 9ee0841..54b9159 100644 --- a/target/nextflow/filter/subset_cosmx/nextflow.config +++ b/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 ├── _exprMat_file.csv\n ├── _fov_positions_file.csv\n ├── _metadata_file.csv\n └── _tx_file.csv \n' author = 'Dorien Roosen, Weiwei Schultz' } diff --git a/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml b/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml index 3983322..83ae401 100644 --- a/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml +++ b/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" diff --git a/target/nextflow/mapping/spaceranger_count/main.nf b/target/nextflow/mapping/spaceranger_count/main.nf index dbe1f6e..44d8bae 100644 --- a/target/nextflow/mapping/spaceranger_count/main.nf +++ b/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" }'''), diff --git a/target/nextflow/mapping/spaceranger_count/nextflow.config b/target/nextflow/mapping/spaceranger_count/nextflow.config index d6b6de0..98f7567 100644 --- a/target/nextflow/mapping/spaceranger_count/nextflow.config +++ b/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' } diff --git a/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml b/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml index 07b4703..2ef77bd 100644 --- a/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml +++ b/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" diff --git a/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf b/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf index 9f256ca..48df415 100644 --- a/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf +++ b/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" : { diff --git a/target/nextflow/workflows/multiomics/spatial_process_samples/nextflow.config b/target/nextflow/workflows/multiomics/spatial_process_samples/nextflow.config index 31394ec..0291d8a 100644 --- a/target/nextflow/workflows/multiomics/spatial_process_samples/nextflow.config +++ b/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' } diff --git a/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml b/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml index ee9b161..6901f97 100644 --- a/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml +++ b/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" diff --git a/target/nextflow/workflows/qc/spatial_qc/main.nf b/target/nextflow/workflows/qc/spatial_qc/main.nf index 0a32572..0bdbd84 100644 --- a/target/nextflow/workflows/qc/spatial_qc/main.nf +++ b/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" : { diff --git a/target/nextflow/workflows/qc/spatial_qc/nextflow.config b/target/nextflow/workflows/qc/spatial_qc/nextflow.config index 50edaa1..7d1289a 100644 --- a/target/nextflow/workflows/qc/spatial_qc/nextflow.config +++ b/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' }