From 932beffdb5b18c098b0b549c0c1245d9061bd727 Mon Sep 17 00:00:00 2001 From: CI Date: Tue, 6 May 2025 20:32:04 +0000 Subject: [PATCH] Build branch main with version main (69c4536) Build pipeline: viash-hub.toolbox.main-5vhb4 Source commit: https://github.com/viash-hub/toolbox/commit/69c4536b849c9a776972a12162376f824b4b4504 Source message: Remove package version from main branch (#14) * remove package version from main branch * update ci --- _viash.yaml | 1 - nextflow.config | 2 +- target/executable/bgzip/.config.vsh.yaml | 10 +++++----- target/executable/bgzip/bgzip | 14 +++++++------- target/executable/yq/.config.vsh.yaml | 10 +++++----- target/executable/yq/yq | 14 +++++++------- target/nextflow/bgzip/.config.vsh.yaml | 10 +++++----- target/nextflow/bgzip/main.nf | 14 +++++++------- target/nextflow/bgzip/nextflow.config | 2 +- target/nextflow/yq/.config.vsh.yaml | 10 +++++----- target/nextflow/yq/main.nf | 14 +++++++------- target/nextflow/yq/nextflow.config | 2 +- 12 files changed, 51 insertions(+), 52 deletions(-) diff --git a/_viash.yaml b/_viash.yaml index 8c9bb98..b1c2c4a 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,5 +1,4 @@ name: toolbox -version: v0.1.0 summary: | A collection of curated command-line tools for general IT tasks, built with Viash. description: | diff --git a/nextflow.config b/nextflow.config index 998e828..5a895df 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,6 +1,6 @@ manifest { name = "toolbox" - version = "v0.1.0" + version = "main" defaultBranch = "main" nextflowVersion = "!>=20.12.1-edge" } diff --git a/target/executable/bgzip/.config.vsh.yaml b/target/executable/bgzip/.config.vsh.yaml index 166770a..8042191 100644 --- a/target/executable/bgzip/.config.vsh.yaml +++ b/target/executable/bgzip/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "bgzip" -version: "v0.1.0" +version: "main" argument_groups: - name: "Inputs" arguments: @@ -210,7 +210,7 @@ engines: id: "docker" image: "quay.io/biocontainers/htslib:1.19--h81da01d_0" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "main" namespace_separator: "/" setup: - type: "docker" @@ -228,11 +228,11 @@ build_info: output: "target/executable/bgzip" executable: "target/executable/bgzip/bgzip" viash_version: "0.9.4" - git_commit: "d33eb370683ba1f1132ec7d7b6884c8040dc901a" + git_commit: "69c4536b849c9a776972a12162376f824b4b4504" git_remote: "https://github.com/viash-hub/toolbox" package_config: name: "toolbox" - version: "v0.1.0" + version: "main" summary: "A collection of curated command-line tools for general IT tasks, built\ \ with Viash.\n" description: "`toolbox` provides a versatile suite of IT components, following the\ @@ -255,7 +255,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".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 := 'main'" keywords: - "toolbox" - "command-line" diff --git a/target/executable/bgzip/bgzip b/target/executable/bgzip/bgzip index 72e59fc..05b8c41 100755 --- a/target/executable/bgzip/bgzip +++ b/target/executable/bgzip/bgzip @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# bgzip v0.1.0 +# bgzip main # # 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 @@ -448,10 +448,10 @@ ENTRYPOINT [] RUN bgzip -h | grep 'Version:' 2>&1 | sed 's/Version:\s\(.*\)/bgzip: "\1"/' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component bgzip" -LABEL org.opencontainers.image.created="2025-05-06T20:10:22Z" +LABEL org.opencontainers.image.created="2025-05-06T20:26:42Z" LABEL org.opencontainers.image.source="https://github.com/samtools/htslib" -LABEL org.opencontainers.image.revision="d33eb370683ba1f1132ec7d7b6884c8040dc901a" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.revision="69c4536b849c9a776972a12162376f824b4b4504" +LABEL org.opencontainers.image.version="main" VIASHDOCKER fi @@ -568,7 +568,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bgzip v0.1.0" + echo "bgzip main" echo "" echo "Block compression/decompression utility" echo "" @@ -674,7 +674,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bgzip v0.1.0" + echo "bgzip main" exit ;; --input) @@ -910,7 +910,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/toolbox/bgzip:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/toolbox/bgzip:main' fi # print dockerfile diff --git a/target/executable/yq/.config.vsh.yaml b/target/executable/yq/.config.vsh.yaml index b99f52e..46ecf4d 100644 --- a/target/executable/yq/.config.vsh.yaml +++ b/target/executable/yq/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "yq" -version: "v0.1.0" +version: "main" argument_groups: - name: "Inputs" arguments: @@ -237,7 +237,7 @@ engines: id: "docker" image: "alpine:latest" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "main" namespace_separator: "/" setup: - type: "apk" @@ -258,11 +258,11 @@ build_info: output: "target/executable/yq" executable: "target/executable/yq/yq" viash_version: "0.9.4" - git_commit: "d33eb370683ba1f1132ec7d7b6884c8040dc901a" + git_commit: "69c4536b849c9a776972a12162376f824b4b4504" git_remote: "https://github.com/viash-hub/toolbox" package_config: name: "toolbox" - version: "v0.1.0" + version: "main" summary: "A collection of curated command-line tools for general IT tasks, built\ \ with Viash.\n" description: "`toolbox` provides a versatile suite of IT components, following the\ @@ -285,7 +285,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".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 := 'main'" keywords: - "toolbox" - "command-line" diff --git a/target/executable/yq/yq b/target/executable/yq/yq index d4927d9..61825ab 100755 --- a/target/executable/yq/yq +++ b/target/executable/yq/yq @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# yq v0.1.0 +# yq main # # 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 @@ -450,10 +450,10 @@ RUN apk add --no-cache bash yq-go RUN /usr/bin/yq --version | sed 's/.*version\sv\(.*\)/yq: "\1"/' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component yq" -LABEL org.opencontainers.image.created="2025-05-06T20:10:22Z" +LABEL org.opencontainers.image.created="2025-05-06T20:26:42Z" LABEL org.opencontainers.image.source="https://github.com/mikefarah/yq" -LABEL org.opencontainers.image.revision="d33eb370683ba1f1132ec7d7b6884c8040dc901a" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.revision="69c4536b849c9a776972a12162376f824b4b4504" +LABEL org.opencontainers.image.version="main" VIASHDOCKER fi @@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "yq v0.1.0" + echo "yq main" echo "" echo "A portable YAML, JSON, XML, CSV, TOML and properties processor" echo "" @@ -659,7 +659,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "yq v0.1.0" + echo "yq main" exit ;; --input) @@ -844,7 +844,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/toolbox/yq:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/toolbox/yq:main' fi # print dockerfile diff --git a/target/nextflow/bgzip/.config.vsh.yaml b/target/nextflow/bgzip/.config.vsh.yaml index 5c2aa39..dfe52b2 100644 --- a/target/nextflow/bgzip/.config.vsh.yaml +++ b/target/nextflow/bgzip/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "bgzip" -version: "v0.1.0" +version: "main" argument_groups: - name: "Inputs" arguments: @@ -210,7 +210,7 @@ engines: id: "docker" image: "quay.io/biocontainers/htslib:1.19--h81da01d_0" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "main" namespace_separator: "/" setup: - type: "docker" @@ -228,11 +228,11 @@ build_info: output: "target/nextflow/bgzip" executable: "target/nextflow/bgzip/main.nf" viash_version: "0.9.4" - git_commit: "d33eb370683ba1f1132ec7d7b6884c8040dc901a" + git_commit: "69c4536b849c9a776972a12162376f824b4b4504" git_remote: "https://github.com/viash-hub/toolbox" package_config: name: "toolbox" - version: "v0.1.0" + version: "main" summary: "A collection of curated command-line tools for general IT tasks, built\ \ with Viash.\n" description: "`toolbox` provides a versatile suite of IT components, following the\ @@ -255,7 +255,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".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 := 'main'" keywords: - "toolbox" - "command-line" diff --git a/target/nextflow/bgzip/main.nf b/target/nextflow/bgzip/main.nf index d262131..24492b4 100644 --- a/target/nextflow/bgzip/main.nf +++ b/target/nextflow/bgzip/main.nf @@ -1,4 +1,4 @@ -// bgzip v0.1.0 +// bgzip main // // 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 @@ -3031,7 +3031,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "bgzip", - "version" : "v0.1.0", + "version" : "main", "argument_groups" : [ { "name" : "Inputs", @@ -3295,7 +3295,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/htslib:1.19--h81da01d_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "main", "namespace_separator" : "/", "setup" : [ { @@ -3317,12 +3317,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bgzip", "viash_version" : "0.9.4", - "git_commit" : "d33eb370683ba1f1132ec7d7b6884c8040dc901a", + "git_commit" : "69c4536b849c9a776972a12162376f824b4b4504", "git_remote" : "https://github.com/viash-hub/toolbox" }, "package_config" : { "name" : "toolbox", - "version" : "v0.1.0", + "version" : "main", "summary" : "A collection of curated command-line tools for general IT tasks, built with Viash.\n", "description" : "`toolbox` provides a versatile suite of IT components, following the robust Viash (https://viash.io) framework.\nThis package focuses on delivering reliable, standalone tools that can be easily integrated into larger computational workflows.\n\nThe core philosophy emphasizes **reusability**, **reproducibility**, and adherence to **best practices** in component creation. Key features of `toolbox` components include:\n\n* **Standalone & Nextflow Ready:** Execute components directly from the command line or seamlessly incorporate them into Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation for each component and its parameters.\n * Full exposure of the underlying tool's arguments for maximum flexibility.\n * Containerized (Docker) to ensure consistent environments and manage dependencies, leading to enhanced reproducibility.\n * Unit tested to verify functionality and ensure reliability.\n", "viash_version" : "0.9.4", @@ -3332,7 +3332,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".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 := 'main'" ], "keywords" : [ "toolbox", @@ -3795,7 +3795,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/toolbox/bgzip", - "tag" : "v0.1.0" + "tag" : "main" }, "tag" : "$id" }'''), diff --git a/target/nextflow/bgzip/nextflow.config b/target/nextflow/bgzip/nextflow.config index bca0d14..29c9435 100644 --- a/target/nextflow/bgzip/nextflow.config +++ b/target/nextflow/bgzip/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bgzip' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'main' description = 'Block compression/decompression utility' } diff --git a/target/nextflow/yq/.config.vsh.yaml b/target/nextflow/yq/.config.vsh.yaml index 560dab0..17be6cd 100644 --- a/target/nextflow/yq/.config.vsh.yaml +++ b/target/nextflow/yq/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "yq" -version: "v0.1.0" +version: "main" argument_groups: - name: "Inputs" arguments: @@ -237,7 +237,7 @@ engines: id: "docker" image: "alpine:latest" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "main" namespace_separator: "/" setup: - type: "apk" @@ -258,11 +258,11 @@ build_info: output: "target/nextflow/yq" executable: "target/nextflow/yq/main.nf" viash_version: "0.9.4" - git_commit: "d33eb370683ba1f1132ec7d7b6884c8040dc901a" + git_commit: "69c4536b849c9a776972a12162376f824b4b4504" git_remote: "https://github.com/viash-hub/toolbox" package_config: name: "toolbox" - version: "v0.1.0" + version: "main" summary: "A collection of curated command-line tools for general IT tasks, built\ \ with Viash.\n" description: "`toolbox` provides a versatile suite of IT components, following the\ @@ -285,7 +285,7 @@ package_config: - ".requirements.commands := ['ps']\n" - ".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 := 'main'" keywords: - "toolbox" - "command-line" diff --git a/target/nextflow/yq/main.nf b/target/nextflow/yq/main.nf index ebcdd96..bcef34d 100644 --- a/target/nextflow/yq/main.nf +++ b/target/nextflow/yq/main.nf @@ -1,4 +1,4 @@ -// yq v0.1.0 +// yq main // // 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 @@ -3031,7 +3031,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "yq", - "version" : "v0.1.0", + "version" : "main", "argument_groups" : [ { "name" : "Inputs", @@ -3301,7 +3301,7 @@ meta = [ "id" : "docker", "image" : "alpine:latest", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "main", "namespace_separator" : "/", "setup" : [ { @@ -3330,12 +3330,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/yq", "viash_version" : "0.9.4", - "git_commit" : "d33eb370683ba1f1132ec7d7b6884c8040dc901a", + "git_commit" : "69c4536b849c9a776972a12162376f824b4b4504", "git_remote" : "https://github.com/viash-hub/toolbox" }, "package_config" : { "name" : "toolbox", - "version" : "v0.1.0", + "version" : "main", "summary" : "A collection of curated command-line tools for general IT tasks, built with Viash.\n", "description" : "`toolbox` provides a versatile suite of IT components, following the robust Viash (https://viash.io) framework.\nThis package focuses on delivering reliable, standalone tools that can be easily integrated into larger computational workflows.\n\nThe core philosophy emphasizes **reusability**, **reproducibility**, and adherence to **best practices** in component creation. Key features of `toolbox` components include:\n\n* **Standalone & Nextflow Ready:** Execute components directly from the command line or seamlessly incorporate them into Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation for each component and its parameters.\n * Full exposure of the underlying tool's arguments for maximum flexibility.\n * Containerized (Docker) to ensure consistent environments and manage dependencies, leading to enhanced reproducibility.\n * Unit tested to verify functionality and ensure reliability.\n", "viash_version" : "0.9.4", @@ -3345,7 +3345,7 @@ meta = [ ".requirements.commands := ['ps']\n", ".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 := 'main'" ], "keywords" : [ "toolbox", @@ -3792,7 +3792,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/toolbox/yq", - "tag" : "v0.1.0" + "tag" : "main" }, "tag" : "$id" }'''), diff --git a/target/nextflow/yq/nextflow.config b/target/nextflow/yq/nextflow.config index aaef2c4..bd4ddcb 100644 --- a/target/nextflow/yq/nextflow.config +++ b/target/nextflow/yq/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'yq' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'main' description = 'A portable YAML, JSON, XML, CSV, TOML and properties processor' }