diff --git a/CHANGELOG.md b/CHANGELOG.md index cd0aec5..bdd2394 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,13 @@ # toolbox unreleased +## MINOR CHANGES + +* Updated the test CI (PR #6). + +* Bump viash to 0.9.0-RC7 (PR #10). + +# toolbox v0.1.0 + ## NEW FEATURES * `bgzip`: Add bgzip functionality to compress and decompress files (initial commit). diff --git a/README.md b/README.md index 09057b1..9af5344 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ License](https://img.shields.io/github/license/viash-hub/toolbox.png)](https://g [![GitHub Issues](https://img.shields.io/github/issues/viash-hub/toolbox.png)](https://github.com/viash-hub/toolbox/issues) [![Viash -version](https://img.shields.io/badge/Viash-v0.9.0--RC6-blue)](https://viash.io) +version](https://img.shields.io/badge/Viash-v0.9.0--RC7-blue)](https://viash.io) A collection of command-line tools. diff --git a/_viash.yaml b/_viash.yaml index 08142f6..55486fb 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -7,7 +7,7 @@ links: issue_tracker: https://github.com/viash-hub/toolbox/issues repository: https://github.com/viash-hub/toolbox -viash_version: 0.9.0-RC6 +viash_version: 0.9.0-RC7 config_mods: | .requirements.commands := ['ps'] diff --git a/src/yq/config.vsh.yaml b/src/yq/config.vsh.yaml index f5bd01a..932fae2 100644 --- a/src/yq/config.vsh.yaml +++ b/src/yq/config.vsh.yaml @@ -16,6 +16,7 @@ argument_groups: direction: input description: files to be processed required: true + example: input.yaml - name: Outputs arguments: - name: --output @@ -23,12 +24,14 @@ argument_groups: direction: output description: output file required: true + example: output.yaml - name: Arguments arguments: - name: --eval type: string description: expression to evaluate required: true + example: '.name = "foo"' - name: --indent type: integer description: sets indent level for output (default 2) diff --git a/target/executable/bgzip/.config.vsh.yaml b/target/executable/bgzip/.config.vsh.yaml index 3022b47..5c2522a 100644 --- a/target/executable/bgzip/.config.vsh.yaml +++ b/target/executable/bgzip/.config.vsh.yaml @@ -225,7 +225,7 @@ build_info: output: "target/executable/bgzip" executable: "target/executable/bgzip/bgzip" viash_version: "0.9.0-RC6" - git_commit: "3eff836ca92b6e13debba8436ad5a484790f8c90" + git_commit: "7cec5cac6937b310c9f172d4c5655a5f20d2442f" git_remote: "https://github.com/viash-hub/toolbox" package_config: name: "toolbox" diff --git a/target/executable/bgzip/bgzip b/target/executable/bgzip/bgzip index f55615d..9e26144 100755 --- a/target/executable/bgzip/bgzip +++ b/target/executable/bgzip/bgzip @@ -508,9 +508,9 @@ 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="2024-07-01T09:02:42Z" +LABEL org.opencontainers.image.created="2024-08-19T07:32:49Z" LABEL org.opencontainers.image.source="https://github.com/samtools/htslib" -LABEL org.opencontainers.image.revision="3eff836ca92b6e13debba8436ad5a484790f8c90" +LABEL org.opencontainers.image.revision="7cec5cac6937b310c9f172d4c5655a5f20d2442f" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/yq/.config.vsh.yaml b/target/executable/yq/.config.vsh.yaml index 30c4bc2..78f761c 100644 --- a/target/executable/yq/.config.vsh.yaml +++ b/target/executable/yq/.config.vsh.yaml @@ -7,6 +7,8 @@ argument_groups: name: "--input" description: "files to be processed" info: null + example: + - "input.yaml" must_exist: true create_parent: true required: true @@ -19,6 +21,8 @@ argument_groups: name: "--output" description: "output file" info: null + example: + - "output.yaml" must_exist: true create_parent: true required: true @@ -31,6 +35,8 @@ argument_groups: name: "--eval" description: "expression to evaluate" info: null + example: + - ".name = \"foo\"" required: true direction: "input" multiple: false @@ -249,7 +255,7 @@ build_info: output: "target/executable/yq" executable: "target/executable/yq/yq" viash_version: "0.9.0-RC6" - git_commit: "3eff836ca92b6e13debba8436ad5a484790f8c90" + git_commit: "7cec5cac6937b310c9f172d4c5655a5f20d2442f" git_remote: "https://github.com/viash-hub/toolbox" package_config: name: "toolbox" diff --git a/target/executable/yq/yq b/target/executable/yq/yq index 888e462..f67a3b2 100755 --- a/target/executable/yq/yq +++ b/target/executable/yq/yq @@ -178,16 +178,19 @@ function ViashHelp { echo "Inputs:" echo " --input" echo " type: file, required parameter, file must exist" + echo " example: input.yaml" echo " files to be processed" echo "" echo "Outputs:" echo " --output" echo " type: file, required parameter, output, file must exist" + echo " example: output.yaml" echo " output file" echo "" echo "Arguments:" echo " --eval" echo " type: string, required parameter" + echo " example: .name = \"foo\"" echo " expression to evaluate" echo "" echo " -I, --indent" @@ -490,9 +493,9 @@ 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="2024-07-01T09:02:43Z" +LABEL org.opencontainers.image.created="2024-08-19T07:32:48Z" LABEL org.opencontainers.image.source="https://github.com/mikefarah/yq" -LABEL org.opencontainers.image.revision="3eff836ca92b6e13debba8436ad5a484790f8c90" +LABEL org.opencontainers.image.revision="7cec5cac6937b310c9f172d4c5655a5f20d2442f" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/nextflow/bgzip/.config.vsh.yaml b/target/nextflow/bgzip/.config.vsh.yaml index 6eba577..8231081 100644 --- a/target/nextflow/bgzip/.config.vsh.yaml +++ b/target/nextflow/bgzip/.config.vsh.yaml @@ -225,7 +225,7 @@ build_info: output: "target/nextflow/bgzip" executable: "target/nextflow/bgzip/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3eff836ca92b6e13debba8436ad5a484790f8c90" + git_commit: "7cec5cac6937b310c9f172d4c5655a5f20d2442f" git_remote: "https://github.com/viash-hub/toolbox" package_config: name: "toolbox" diff --git a/target/nextflow/bgzip/main.nf b/target/nextflow/bgzip/main.nf index 441b925..2764f8e 100644 --- a/target/nextflow/bgzip/main.nf +++ b/target/nextflow/bgzip/main.nf @@ -3061,7 +3061,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bgzip", "viash_version" : "0.9.0-RC6", - "git_commit" : "3eff836ca92b6e13debba8436ad5a484790f8c90", + "git_commit" : "7cec5cac6937b310c9f172d4c5655a5f20d2442f", "git_remote" : "https://github.com/viash-hub/toolbox" }, "package_config" : { diff --git a/target/nextflow/yq/.config.vsh.yaml b/target/nextflow/yq/.config.vsh.yaml index c504a80..aa723be 100644 --- a/target/nextflow/yq/.config.vsh.yaml +++ b/target/nextflow/yq/.config.vsh.yaml @@ -7,6 +7,8 @@ argument_groups: name: "--input" description: "files to be processed" info: null + example: + - "input.yaml" must_exist: true create_parent: true required: true @@ -19,6 +21,8 @@ argument_groups: name: "--output" description: "output file" info: null + example: + - "output.yaml" must_exist: true create_parent: true required: true @@ -31,6 +35,8 @@ argument_groups: name: "--eval" description: "expression to evaluate" info: null + example: + - ".name = \"foo\"" required: true direction: "input" multiple: false @@ -249,7 +255,7 @@ build_info: output: "target/nextflow/yq" executable: "target/nextflow/yq/main.nf" viash_version: "0.9.0-RC6" - git_commit: "3eff836ca92b6e13debba8436ad5a484790f8c90" + git_commit: "7cec5cac6937b310c9f172d4c5655a5f20d2442f" git_remote: "https://github.com/viash-hub/toolbox" package_config: name: "toolbox" diff --git a/target/nextflow/yq/main.nf b/target/nextflow/yq/main.nf index 31ab283..60775ee 100644 --- a/target/nextflow/yq/main.nf +++ b/target/nextflow/yq/main.nf @@ -2788,6 +2788,9 @@ meta = [ "type" : "file", "name" : "--input", "description" : "files to be processed", + "example" : [ + "input.yaml" + ], "must_exist" : true, "create_parent" : true, "required" : true, @@ -2804,6 +2807,9 @@ meta = [ "type" : "file", "name" : "--output", "description" : "output file", + "example" : [ + "output.yaml" + ], "must_exist" : true, "create_parent" : true, "required" : true, @@ -2820,6 +2826,9 @@ meta = [ "type" : "string", "name" : "--eval", "description" : "expression to evaluate", + "example" : [ + ".name = \\"foo\\"" + ], "required" : true, "direction" : "input", "multiple" : false, @@ -3065,7 +3074,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/yq", "viash_version" : "0.9.0-RC6", - "git_commit" : "3eff836ca92b6e13debba8436ad5a484790f8c90", + "git_commit" : "7cec5cac6937b310c9f172d4c5655a5f20d2442f", "git_remote" : "https://github.com/viash-hub/toolbox" }, "package_config" : { diff --git a/target/nextflow/yq/nextflow_schema.json b/target/nextflow/yq/nextflow_schema.json index 0a0ed2b..3d7ba38 100644 --- a/target/nextflow/yq/nextflow_schema.json +++ b/target/nextflow/yq/nextflow_schema.json @@ -17,8 +17,8 @@ "input": { "type": "string", - "description": "Type: `file`, required. files to be processed", - "help_text": "Type: `file`, required. files to be processed" + "description": "Type: `file`, required, example: `input.yaml`. files to be processed", + "help_text": "Type: `file`, required, example: `input.yaml`. files to be processed" } @@ -37,10 +37,10 @@ "output": { "type": "string", - "description": "Type: `file`, required, default: `$id.$key.output.output`. output file", - "help_text": "Type: `file`, required, default: `$id.$key.output.output`. output file" + "description": "Type: `file`, required, default: `$id.$key.output.yaml`, example: `output.yaml`. output file", + "help_text": "Type: `file`, required, default: `$id.$key.output.yaml`, example: `output.yaml`. output file" , - "default": "$id.$key.output.output" + "default": "$id.$key.output.yaml" } @@ -58,8 +58,8 @@ "eval": { "type": "string", - "description": "Type: `string`, required. expression to evaluate", - "help_text": "Type: `string`, required. expression to evaluate" + "description": "Type: `string`, required, example: `.name = \"foo\"`. expression to evaluate", + "help_text": "Type: `string`, required, example: `.name = \"foo\"`. expression to evaluate" }