diff --git a/.vscode/viash_config.yaml b/.vscode/viash_config.yaml index b7a6aabd..d416f28f 100644 --- a/.vscode/viash_config.yaml +++ b/.vscode/viash_config.yaml @@ -7,29 +7,51 @@ definitions: \ you choose. \n" type: "object" properties: + project_config: + description: "The project config content used during build." + $ref: "#/definitions/ProjectConfig" + info: + $ref: "#/definitions/Info" + platforms: + description: "A list of platforms to generate target artifacts for.\n\n -\ + \ Native\n - Docker\n - Nextflow\n" + type: "array" + items: + $ref: "#/definitions/Platform" + engines: + description: "A list of engine environments to execute target artifacts in.\n\ + \n - NativeEngine\n - DockerEngine\n" + type: "array" + items: + $ref: "#/definitions/Engine" functionality: description: "The functionality describes the behaviour of the script in terms\ \ of arguments and resources.\nBy specifying a few restrictions (e.g. mandatory\ \ arguments) and adding some descriptions, Viash will automatically generate\ \ a stylish command-line interface for you.\n" $ref: "#/definitions/Functionality" - platforms: - description: "A list of platforms to generate target artifacts for.\n\n -\ - \ Native\n - Docker\n - Nextflow\n" + runners: + description: "A list of runners to execute target artifacts.\n\n - ExecutableRunner\n\ + \ - NextflowRunner\n" type: "array" items: - $ref: "#/definitions/Platform" + $ref: "#/definitions/Runner" required: - "functionality" - - "platforms" additionalProperties: false - Project: + ProjectConfig: description: "A Viash project configuration file. It's name should be `_viash.yaml`." type: "object" properties: + name: + description: "The name of the project." + type: "string" source: description: "Which source directory to use for the `viash ns` commands." type: "string" + description: + description: "A description of the project." + type: "string" viash_version: description: "Which version of Viash to use." type: "string" @@ -41,11 +63,90 @@ definitions: items: description: "Which config mods to apply." type: "string" + info: + description: "Structured information. Can be any shape: a string, vector,\ + \ map or even nested map." + type: "object" + license: + description: "The license of the project." + type: "string" + authors: + description: "The authors of the project." + type: "array" + items: + $ref: "#/definitions/Author" + repositories: + description: "Common repository definitions for component dependencies." + type: "array" + items: + $ref: "#/definitions/RepositoryWithName" + keywords: + description: "The keywords of the project." + type: "array" + items: + type: "string" target: description: "Which target directory to use for `viash ns build`." type: "string" + reference: + description: "References to external resources related to the project." + $ref: "#/definitions/ProjectConfigReferences" + organization: + description: "The organization of the project." + type: "string" + version: + description: "The version of the project." + type: "string" + links: + description: "External links of the project." + $ref: "#/definitions/ProjectConfigLinks" + required: [] + additionalProperties: false + ProjectConfigLinks: + description: "Links to external resources related to the project." + type: "object" + properties: + repository: + description: "Source repository url." + type: "string" + documentation: + description: "Documentation website url." + type: "string" + docker_registry: + description: "Docker registry url." + type: "string" + homepage: + description: "Homepage website url." + type: "string" + issue_tracker: + description: "Issue tracker url." + type: "string" required: [] additionalProperties: false + ProjectConfigReferences: + description: "References to external resources related to the project." + type: "object" + properties: + bibtex: + oneOf: + - description: "One or multiple BibTeX reference(s) of the project." + type: "string" + - type: "array" + items: + description: "One or multiple BibTeX reference(s) of the project." + type: "string" + doi: + oneOf: + - description: "One or multiple DOI reference(s) of the project." + type: "string" + - type: "array" + items: + description: "One or multiple DOI reference(s) of the project." + type: "string" + required: + - "bibtex" + - "doi" + additionalProperties: false Info: description: "Meta information fields filled in by Viash during build." type: "object" @@ -59,41 +160,26 @@ definitions: viash_version: description: "The Viash version that was used to build the component." type: "string" - config: - description: "Path to the config used during build." - type: "string" output: description: "Folder path to the build artifacts." type: "string" - platform: - description: "The platform id used during build." - type: "string" git_commit: description: "Git commit hash." type: "string" executable: description: "Output folder with main executable path." type: "string" - required: - - "config" - additionalProperties: false - EnvironmentVariables: - description: "Viash checks several environment variables during operation." - type: "object" - properties: - VIASH_VERSION: - description: "A specific Viash version can be set to run the commands with.\ - \ If so required, the specific Viash version will be downloaded.\nThis is\ - \ useful when replicating older results or building Viash components that\ - \ use outdated code.\n" + engine: + description: "The engine id used during build." + type: "string" + runner: + description: "The runner id used during build." type: "string" - VIASH_HOME: - description: "If `VIASH_HOME` is not defined, the fallback `HOME`/.viash is\ - \ used.\n\nLocation where specific downloaded versions of Viash will be\ - \ cached and run from.\n" + config: + description: "Path to the config used during build." type: "string" required: - - "VIASH_HOME" + - "config" additionalProperties: false Functionality: description: "The functionality-part of the config file describes the behaviour\ @@ -102,6 +188,9 @@ definitions: \ generate a stylish command-line interface for you.\n" type: "object" properties: + organization: + description: "The organization of the project." + type: "string" name: description: "Name of the component and the filename of the executable when\ \ built with `viash build`." @@ -110,6 +199,9 @@ definitions: description: "Structured information. Can be any shape: a string, vector,\ \ map or even nested map." type: "object" + license: + description: "The license of the project." + type: "string" version: description: "Version of the component. This field will be used to version\ \ the executable and the Docker container." @@ -149,25 +241,6 @@ definitions: type: "array" items: $ref: "#/definitions/RepositoryWithName" - resources: - description: "Resources are files that support the component. The first resource\ - \ should be a script that will be executed when the functionality is run.\ - \ Additional resources will be copied to the same directory.\n\nCommon properties:\n\ - \n * type: `file` / `r_script` / `python_script` / `bash_script` / `javascript_script`\ - \ / `scala_script` / `csharp_script`, specifies the type of the resource.\ - \ The first resource cannot be of type `file`. When the type is not specified,\ - \ the default type is simply `file`.\n * dest: filename, the resulting name\ - \ of the resource. From within a script, the file can be accessed at `meta[\"\ - resources_dir\"] + \"/\" + dest`. If unspecified, `dest` will be set to\ - \ the basename of the `path` parameter.\n * path: `path/to/file`, the path\ - \ of the input file. Can be a relative or an absolute path, or a URI. Mutually\ - \ exclusive with `text`.\n * text: ...multiline text..., the content of\ - \ the resulting file specified as a string. Mutually exclusive with `path`.\n\ - \ * is_executable: `true` / `false`, whether the resulting resource file\ - \ should be made executable.\n" - type: "array" - items: - $ref: "#/definitions/Resource" test_resources: description: "One or more scripts to be used to test the component behaviour\ \ when `viash test` is invoked. Additional files of type `file` will be\ @@ -200,6 +273,30 @@ definitions: description: "A description on how to use the component. This will be displayed\ \ with `--help` under the 'Usage:' section." type: "string" + resources: + description: "Resources are files that support the component. The first resource\ + \ should be a script that will be executed when the functionality is run.\ + \ Additional resources will be copied to the same directory.\n\nCommon properties:\n\ + \n * type: `file` / `r_script` / `python_script` / `bash_script` / `javascript_script`\ + \ / `scala_script` / `csharp_script`, specifies the type of the resource.\ + \ The first resource cannot be of type `file`. When the type is not specified,\ + \ the default type is simply `file`.\n * dest: filename, the resulting name\ + \ of the resource. From within a script, the file can be accessed at `meta[\"\ + resources_dir\"] + \"/\" + dest`. If unspecified, `dest` will be set to\ + \ the basename of the `path` parameter.\n * path: `path/to/file`, the path\ + \ of the input file. Can be a relative or an absolute path, or a URI. Mutually\ + \ exclusive with `text`.\n * text: ...multiline text..., the content of\ + \ the resulting file specified as a string. Mutually exclusive with `path`.\n\ + \ * is_executable: `true` / `false`, whether the resulting resource file\ + \ should be made executable.\n" + type: "array" + items: + $ref: "#/definitions/Resource" + keywords: + description: "The keywords of the components." + type: "array" + items: + type: "string" namespace: description: "Namespace this component is a part of. See the Namespaces guide\ \ for more information on namespaces." @@ -288,6 +385,253 @@ definitions: - "name" - "arguments" additionalProperties: false + Runner: + oneOf: + - $ref: "#/definitions/ExecutableRunner" + - $ref: "#/definitions/NextflowRunner" + ExecutableRunner: + description: "Run code as an executable.\n\nThis runner is the default runner.\ + \ It will generate a bash script that can be run directly.\n\nThis runner is\ + \ also used for the native engine.\n\nThis runner is also used for the docker\ + \ engine.\n" + type: "object" + properties: + docker_setup_strategy: + description: "The Docker setup strategy to use when building a docker engine\ + \ enrivonment.\n\n| Strategy | Description |\n|-----|----------|\n| `alwaysbuild`\ + \ / `build` / `b` | Always build the image from the dockerfile. This is\ + \ the default setup strategy.\n| `alwayscachedbuild` / `cachedbuild` / `cb`\ + \ | Always build the image from the dockerfile, with caching enabled.\n\ + | `ifneedbebuild` | Build the image if it does not exist locally.\n| `ifneedbecachedbuild`\ + \ | Build the image with caching enabled if it does not exist locally, with\ + \ caching enabled.\n| `alwayspull` / `pull` / `p` | Try to pull the container\ + \ from [Docker Hub](https://hub.docker.com) or the specified docker registry.\n\ + | `alwayspullelsebuild` / `pullelsebuild` | Try to pull the image from\ + \ a registry and build it if it doesn't exist.\n| `alwayspullelsecachedbuild`\ + \ / `pullelsecachedbuild` | Try to pull the image from a registry and build\ + \ it with caching if it doesn't exist.\n| `ifneedbepull` | If the image\ + \ does not exist locally, pull the image.\n| `ifneedbepullelsebuild` | \ + \ If the image does not exist locally, pull the image. If the image does\ + \ exist, build it.\n| `ifneedbepullelsecachedbuild` | If the image does\ + \ not exist locally, pull the image. If the image does exist, build it with\ + \ caching enabled.\n| `push` | Push the container to [Docker Hub](https://hub.docker.com)\ + \ or the specified docker registry.\n| `pushifnotpresent` | Push the container\ + \ to [Docker Hub](https://hub.docker.com) or the specified docker registry\ + \ if the tag does not exist yet.\n| `donothing` / `meh` | Do not build or\ + \ pull anything.\n\n" + $ref: "#/definitions/DockerSetupStrategy" + workdir: + description: "The working directory when starting the engine. This doesn't\ + \ change the Dockerfile but gets added as a command-line argument at runtime." + type: "string" + docker_run_args: + oneOf: + - description: "Provide runtime arguments to Docker. See the documentation\ + \ on [`docker run`](https://docs.docker.com/engine/reference/run/) for\ + \ more information." + type: "string" + - type: "array" + items: + description: "Provide runtime arguments to Docker. See the documentation\ + \ on [`docker run`](https://docs.docker.com/engine/reference/run/) for\ + \ more information." + type: "string" + id: + description: "Name of the runner. As with all runners, you can give an runner\ + \ a different name. By specifying `id: foo`, you can target this executor\ + \ (only) by specifying `...` in any of the Viash commands." + type: "string" + port: + oneOf: + - description: "A list of enabled ports. This doesn't change the Dockerfile\ + \ but gets added as a command-line argument at runtime." + type: "integer" + - description: "A list of enabled ports. This doesn't change the Dockerfile\ + \ but gets added as a command-line argument at runtime." + type: "string" + - description: "A list of enabled ports. This doesn't change the Dockerfile\ + \ but gets added as a command-line argument at runtime." + type: "array" + items: + type: "integer" + - description: "A list of enabled ports. This doesn't change the Dockerfile\ + \ but gets added as a command-line argument at runtime." + type: "array" + items: + type: "string" + type: + description: "Run code as an executable.\n\nThis runner is the default runner.\ + \ It will generate a bash script that can be run directly.\n\nThis runner\ + \ is also used for the native engine.\n\nThis runner is also used for the\ + \ docker engine.\n" + const: "executable" + required: + - "type" + additionalProperties: false + NextflowRunner: + description: "Run a Viash component on a Nextflow backend engine.\n" + type: "object" + properties: + auto: + description: "Automated processing flags which can be toggled on or off:\n\ + \n| Flag | Description | Default |\n|---|---------|----|\n| `simplifyInput`\ + \ | If `true`, an input tuple only containing only a single File (e.g. `[\"\ + foo\", file(\"in.h5ad\")]`) is automatically transformed to a map (i.e.\ + \ `[\"foo\", [ input: file(\"in.h5ad\") ] ]`). | `true` |\n| `simplifyOutput`\ + \ | If `true`, an output tuple containing a map with a File (e.g. `[\"foo\"\ + , [ output: file(\"out.h5ad\") ] ]`) is automatically transformed to a map\ + \ (i.e. `[\"foo\", file(\"out.h5ad\")]`). | `false` |\n| `transcript` |\ + \ If `true`, the module's transcripts from `work/` are automatically published\ + \ to `params.transcriptDir`. If not defined, `params.publishDir + \"/_transcripts\"\ + ` will be used. Will throw an error if neither are defined. | `false` |\n\ + | `publish` | If `true`, the module's outputs are automatically published\ + \ to `params.publishDir`. If equal to \"state\", also a `.state.yaml` file\ + \ will be published in the publish dir. Will throw an error if `params.publishDir`\ + \ is not defined. | `false` |\n\n" + $ref: "#/definitions/NextflowAuto" + directives: + description: "Directives are optional settings that affect the execution of\ + \ the process. These mostly match up with the Nextflow counterparts. \n" + $ref: "#/definitions/NextflowDirectives" + container: + description: "Specifies the Docker engine id to be used to run Nextflow." + type: "string" + config: + description: "Allows tweaking how the Nextflow Config file is generated." + $ref: "#/definitions/NextflowConfig" + debug: + description: "Whether or not to print debug messages." + type: "boolean" + id: + description: "Name of the runner. As with all runners, you can give an runner\ + \ a different name. By specifying `id: foo`, you can target this runner\ + \ (only) by specifying `...` in any of the Viash commands." + type: "string" + type: + description: "Run a Viash component on a Nextflow backend engine.\n" + const: "nextflow" + required: + - "type" + additionalProperties: false + Engine: + oneOf: + - $ref: "#/definitions/DockerEngine" + - $ref: "#/definitions/NativeEngine" + NativeEngine: + description: "Running a Viash component on a native engine means that the script\ + \ will be executed in your current environment.\nAny dependencies are assumed\ + \ to have been installed by the user, so the native engine is meant for developers\ + \ (who know what they're doing) or for simple bash scripts (which have no extra\ + \ dependencies).\n" + type: "object" + properties: + id: + description: "Name of the engine. As with all engines, you can give an engine\ + \ a different name. By specifying `id: foo`, you can target this engine\ + \ (only) by specifying `...` in any of the Viash commands." + type: "string" + type: + description: "Running a Viash component on a native engine means that the\ + \ script will be executed in your current environment.\nAny dependencies\ + \ are assumed to have been installed by the user, so the native engine is\ + \ meant for developers (who know what they're doing) or for simple bash\ + \ scripts (which have no extra dependencies).\n" + const: "native" + required: + - "type" + additionalProperties: false + DockerEngine: + description: "Run a Viash component on a Docker backend engine.\nBy specifying\ + \ which dependencies your component needs, users will be able to build a docker\ + \ container from scratch using the setup flag, or pull it from a docker repository.\n" + type: "object" + properties: + organization: + description: "Name of a container's [organization](https://docs.docker.com/docker-hub/orgs/)." + type: "string" + registry: + description: "The URL to the a [custom Docker registry](https://docs.docker.com/registry/)" + type: "string" + image: + description: "The base container to start from. You can also add the tag here\ + \ if you wish." + type: "string" + tag: + description: "Specify a Docker image based on its tag." + type: "string" + target_image: + description: "If anything is specified in the setup section, running the `---setup`\ + \ will result in an image with the name of `:`. If\ + \ nothing is specified in the `setup` section, simply `image` will be used.\ + \ Advanced usage only." + type: "string" + target_tag: + description: "The tag the resulting image gets. Advanced usage only." + type: "string" + namespace_separator: + description: "The separator between the namespace and the name of the component,\ + \ used for determining the image name. Default: \"/\"." + type: "string" + id: + description: "Name of the engine. As with all engines, you can give a engine\ + \ a different name. By specifying `id: foo`, you can target this engine\ + \ (only) by specifying `...` in any of the Viash commands." + type: "string" + target_registry: + description: "The URL where the resulting image will be pushed to. Advanced\ + \ usage only." + type: "string" + type: + description: "Run a Viash component on a Docker backend engine.\nBy specifying\ + \ which dependencies your component needs, users will be able to build a\ + \ docker container from scratch using the setup flag, or pull it from a\ + \ docker repository.\n" + const: "docker" + target_organization: + description: "The organization set in the resulting image. Advanced usage\ + \ only." + type: "string" + setup: + description: "A list of requirements for installing the following types of\ + \ packages:\n\n - apt\n - apk\n - Docker setup instructions\n - JavaScript\n\ + \ - Python\n - R\n - Ruby\n - yum\n\nThe order in which these dependencies\ + \ are specified determines the order in which they will be installed.\n" + type: "array" + items: + $ref: "#/definitions/Requirements" + cmd: + oneOf: + - description: "Set the default command being executed when running the Docker\ + \ container." + type: "string" + - description: "Set the default command being executed when running the Docker\ + \ container." + type: "array" + items: + type: "string" + target_image_source: + description: "The source of the target image. This is used for defining labels\ + \ in the dockerfile." + type: "string" + test_setup: + description: "Additional requirements specific for running unit tests." + type: "array" + items: + $ref: "#/definitions/Requirements" + entrypoint: + oneOf: + - description: "Override the entrypoint of the base container. Default set\ + \ `ENTRYPOINT []`." + type: "string" + - description: "Override the entrypoint of the base container. Default set\ + \ `ENTRYPOINT []`." + type: "array" + items: + type: "string" + required: + - "image" + - "type" + additionalProperties: false Platform: oneOf: - $ref: "#/definitions/NativePlatform" @@ -356,6 +700,16 @@ definitions: description: "Enables or disables automatic volume mapping. Enabled when set\ \ to `Automatic` or disabled when set to `Manual`. Default: `Automatic`." $ref: "#/definitions/DockerResolveVolume" + cmd: + oneOf: + - description: "Set the default command being executed when running the Docker\ + \ container." + type: "string" + - description: "Set the default command being executed when running the Docker\ + \ container." + type: "array" + items: + type: "string" id: description: "As with all platforms, you can give a platform a different name.\ \ By specifying `id: foo`, you can target this platform (only) by specifying\ @@ -366,19 +720,15 @@ definitions: - description: "A list of enabled ports. This doesn't change the Dockerfile\ \ but gets added as a command-line argument at runtime." type: "string" - - description: "A list of enabled ports. This doesn't change the Dockerfile\ - \ but gets added as a command-line argument at runtime." - type: "integer" - - description: "A list of enabled ports. This doesn't change the Dockerfile\ - \ but gets added as a command-line argument at runtime." - type: "array" + - type: "array" items: + description: "A list of enabled ports. This doesn't change the Dockerfile\ + \ but gets added as a command-line argument at runtime." type: "string" - - description: "A list of enabled ports. This doesn't change the Dockerfile\ - \ but gets added as a command-line argument at runtime." - type: "array" - items: - type: "integer" + target_registry: + description: "The URL where the resulting image will be pushed to. Advanced\ + \ usage only." + type: "string" setup: description: "A list of requirements for installing the following types of\ \ packages:\n\n - apt\n - apk\n - Docker setup instructions\n - JavaScript\n\ @@ -397,16 +747,6 @@ definitions: \ nothing is specified in the `setup` section, simply `image` will be used.\ \ Advanced usage only." type: "string" - cmd: - oneOf: - - description: "Set the default command being executed when running the Docker\ - \ container." - type: "string" - - description: "Set the default command being executed when running the Docker\ - \ container." - type: "array" - items: - type: "string" target_image_source: description: "The source of the target image. This is used for defining labels\ \ in the dockerfile." @@ -426,10 +766,6 @@ definitions: type: "array" items: type: "string" - target_registry: - description: "The URL where the resulting image will be pushed to. Advanced\ - \ usage only." - type: "string" setup_strategy: description: "The Docker setup strategy to use when building a container.\n\ \n| Strategy | Description |\n|-----|----------|\n| `alwaysbuild` / `build`\ @@ -464,13 +800,6 @@ definitions: description: "The organization set in the resulting image. Advanced usage\ \ only." type: "string" - chown: - description: "In Linux, files created by a Docker container will be owned\ - \ by `root`. With `chown: true`, Viash will automatically change the ownership\ - \ of output files (arguments with `type: file` and `direction: output`)\ - \ to the user running the Viash command after execution of the component.\ - \ Default value: `true`." - type: "boolean" required: - "image" - "type" @@ -969,6 +1298,8 @@ definitions: \ -t`\n - `trim` is an argument, which can be passed with `executable_name\ \ trim` \n" type: "string" + direction: + $ref: "#/definitions/Direction" info: description: "Structured information. Can be any shape: a string, vector,\ \ map or even nested map." @@ -1040,6 +1371,8 @@ definitions: \ -s`\n - `silent` is an argument, which can be passed with `executable_name\ \ silent` \n" type: "string" + direction: + $ref: "#/definitions/Direction" info: description: "Structured information. Can be any shape: a string, vector,\ \ map or even nested map." @@ -1078,6 +1411,8 @@ definitions: \ -n`\n - `no-log` is an argument, which can be passed with `executable_name\ \ no-log` \n" type: "string" + direction: + $ref: "#/definitions/Direction" info: description: "Structured information. Can be any shape: a string, vector,\ \ map or even nested map." @@ -1155,6 +1490,8 @@ definitions: \ value is lower than the minimum, an error will be produced. Can be combined\ \ with [`max`](#max) to clamp values." $ref: "#/definitions/DoubleWithInf" + direction: + $ref: "#/definitions/Direction" multiple: description: "Treat the argument value as an array. Arrays can be passed using\ \ the delimiter `--foo=1:2:3` or by providing the same argument multiple\ @@ -1323,6 +1660,8 @@ definitions: \ value is lower than the minimum, an error will be produced. Can be combined\ \ with [`max`](#max) to clamp values." type: "integer" + direction: + $ref: "#/definitions/Direction" multiple: description: "Treat the argument value as an array. Arrays can be passed using\ \ the delimiter `--foo=1:2:3` or by providing the same argument multiple\ @@ -1409,6 +1748,8 @@ definitions: \ value is lower than the minimum, an error will be produced. Can be combined\ \ with [`max`](#max) to clamp values." type: "integer" + direction: + $ref: "#/definitions/Direction" multiple: description: "Treat the argument value as an array. Arrays can be passed using\ \ the delimiter `--foo=1:2:3` or by providing the same argument multiple\ @@ -1455,6 +1796,8 @@ definitions: type: "array" items: type: "string" + direction: + $ref: "#/definitions/Direction" info: description: "Structured information. Can be any shape: a string, vector,\ \ map or even nested map." diff --git a/_viash.yaml b/_viash.yaml index c59f8543..b4133db8 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1 +1 @@ -viash_version: 0.8.4 \ No newline at end of file +viash_version: 0.9.0-RC1 \ No newline at end of file diff --git a/src/arriba/config.vsh.yaml b/src/arriba/config.vsh.yaml index 601ad6c2..2439af57 100644 --- a/src/arriba/config.vsh.yaml +++ b/src/arriba/config.vsh.yaml @@ -1,13 +1,14 @@ functionality: name: arriba description: Detect gene fusions from RNA-Seq data - info: - keywords: [Gene fusion, RNA-Seq] + keywords: [Gene fusion, RNA-Seq] + links: homepage: https://arriba.readthedocs.io/en/latest/ documentation: https://arriba.readthedocs.io/en/latest/ repository: https://github.com/suhrig/arriba - reference: "doi:10.1101/gr.257246.119" - licence: MIT + reference: + doi: 10.1101/gr.257246.119 + license: MIT requirements: cpus: 1 commands: [ arriba ] @@ -376,11 +377,13 @@ functionality: path: test.sh - type: file path: test_data -platforms: +engines: - type: docker image: quay.io/biocontainers/arriba:2.4.0--h0033a41_2 setup: - type: docker run: | arriba -h | grep 'Version:' 2>&1 | sed 's/Version:\s\(.*\)/arriba: "\1"/' > /var/software_versions.txt - - type: nextflow +runners: + - type: executable + - type: nextflow \ No newline at end of file diff --git a/src/bgzip/config.vsh.yaml b/src/bgzip/config.vsh.yaml index 6a5e7f49..95f2d6a1 100644 --- a/src/bgzip/config.vsh.yaml +++ b/src/bgzip/config.vsh.yaml @@ -1,11 +1,11 @@ functionality: name: bgzip description: Block compression/decompression utility - info: + links: homepage: https://www.htslib.org/ documentation: https://www.htslib.org/doc/bgzip.html repository: https://github.com/samtools/htslib - licence: MIT + license: MIT requirements: commands: [ bgzip ] argument_groups: @@ -115,11 +115,13 @@ functionality: - type: file path: test_data -platforms: +engines: - type: docker image: quay.io/biocontainers/htslib:1.19--h81da01d_0 setup: - type: docker run: | bgzip -h | grep 'Version:' 2>&1 | sed 's/Version:\s\(.*\)/bgzip: "\1"/' > /var/software_versions.txt +runners: + - type: executable - type: nextflow \ No newline at end of file diff --git a/src/busco/config.vsh.yaml b/src/busco/config.vsh.yaml index fba14892..d1686c3f 100644 --- a/src/busco/config.vsh.yaml +++ b/src/busco/config.vsh.yaml @@ -1,13 +1,14 @@ functionality: name: busco description: Assessment of genome assembly and annotation completeness with single copy orthologs - info: - keywords: [Genome assembly, quality control] + keywords: [Genome assembly, quality control] + links: homepage: https://busco.ezlab.org/ documentation: https://busco.ezlab.org/busco_userguide.html repository: https://gitlab.com/ezlab/busco - reference: "10.1007/978-1-4939-9173-0_14" - licence: MIT + reference: + doi: "10.1007/978-1-4939-9173-0_14" + license: MIT argument_groups: - name: Inputs arguments: @@ -199,11 +200,13 @@ functionality: path: test.sh - type: file path: test_data -platforms: +engines: - type: docker image: quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0 setup: - type: docker run: | busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_versions.txt +runners: + - type: executable - type: nextflow diff --git a/src/fastp/config.vsh.yaml b/src/fastp/config.vsh.yaml index c513ec92..3ccef8cd 100644 --- a/src/fastp/config.vsh.yaml +++ b/src/fastp/config.vsh.yaml @@ -20,12 +20,13 @@ functionality: - support reading from STDIN and writing to STDOUT - support interleaved input - support ultra-fast FASTQ-level deduplication - info: - keywords: [RNA-Seq, Trimming, Quality control] + keywords: [RNA-Seq, Trimming, Quality control] + links: repository: https://github.com/OpenGene/fastp documentation: https://github.com/OpenGene/fastp/blob/master/README.md - reference: "doi:10.1093/bioinformatics/bty560" - licence: MIT + reference: + doi: "10.1093/bioinformatics/bty560" + licence: MIT argument_groups: - name: Inputs description: | @@ -564,11 +565,13 @@ functionality: path: test.sh - type: file path: test_data -platforms: +engines: - type: docker image: quay.io/biocontainers/fastp:0.23.4--hadf994f_2 setup: - type: docker run: | fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /var/software_versions.txt +runners: + - type: executable - type: nextflow diff --git a/src/featurecounts/config.vsh.yaml b/src/featurecounts/config.vsh.yaml index 8a2002d4..d9b2442c 100644 --- a/src/featurecounts/config.vsh.yaml +++ b/src/featurecounts/config.vsh.yaml @@ -2,13 +2,14 @@ functionality: name: featurecounts description: | featureCounts is a read summarization program for counting reads generated from either RNA or genomic DNA sequencing experiments by implementing highly efficient chromosome hashing and feature blocking techniques. It works with either single or paired-end reads and provides a wide range of options appropriate for different sequencing applications. - info: - keywords: ["Read counting", "Genomic features"] + keywords: ["Read counting", "Genomic features"] + links: homepage: https://subread.sourceforge.net/ documentation: https://subread.sourceforge.net/SubreadUsersGuide.pdf repository: https://github.com/ShiLab-Bioinformatics/subread - reference: "doi:10.1093/bioinformatics/btt656" - licence: GPL-3.0 + reference: + doi: "10.1093/bioinformatics/btt656" + licence: GPL-3.0 requirements: commands: [ featureCounts ] @@ -327,11 +328,13 @@ functionality: - type: file path: test_data -platforms: +engines: - type: docker image: quay.io/biocontainers/subread:2.0.6--he4a0461_0 setup: - type: docker run: | featureCounts -v 2>&1 | sed 's/featureCounts v\([0-9.]*\)/featureCounts: \1/' > /var/software_versions.txt +runners: + - type: executable - type: nextflow \ No newline at end of file