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Merged
mashehu merged 5 commits into from
Dec 4, 2025
Merged

meta.yml schema: add containers section, fix order and simplify #9503

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20b8659
fix order
mashehu Dec 4, 2025
958e6bf
add container section
mashehu Dec 4, 2025
7e878d0
simplify schema
mashehu Dec 4, 2025
8176a85
require https for singluarity
mashehu Dec 4, 2025
8407e83
Merge branch 'master' into add-container-to-meta-yml-schema
mashehu Dec 4, 2025
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299 changes: 167 additions & 132 deletions modules/meta-schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -24,124 +24,6 @@
"uniqueItems": true,
"minItems": 3
},
"authors": {
"type": "array",
"description": "Authors of the module",
"items": {
"type": "string"
}
},
"maintainers": {
"type": "array",
"description": "Maintainers of the module",
"items": {
"type": "string"
}
},
"extra_args": {
"type": "array",
"description": "Extra arguments for the module",
"items": {
"type": "object",
"properties": {
"description": {
"type": "string",
"description": "Description of the argument"
}
}
}
},
"input": {
"type": "array",
"description": "Input channels for the module",
"items": {
"oneOf": [
{
"type": "array",
"items": {
"type": "object",
"patternProperties": {
".*": {
"$ref": "#/definitions/elementProperties"
}
}
}
},
{
"type": "object",
"patternProperties": {
".*": {
"$ref": "#/definitions/elementProperties"
}
}
}
]
}
},
"output": {
"type": "object",
"description": "Output channels for the module",
"patternProperties": {
".*": {
"type": "array",
"items": {
"oneOf": [
{
"type": "object",
"patternProperties": {
".*": {
"$ref": "#/definitions/elementProperties"
}
}
},
{
"type": "array",
"items": {
"type": "object",
"patternProperties": {
".*": {
"$ref": "#/definitions/elementProperties"
}
}
}
}
]
}
}
}
},
"topics": {
"type": "object",
"description": "Topics of the module",
"patternProperties": {
".*": {
"type": "array",
"items": {
"oneOf": [
{
"type": "object",
"patternProperties": {
".*": {
"$ref": "#/definitions/elementProperties"
}
}
},
{
"type": "array",
"items": {
"type": "object",
"patternProperties": {
".*": {
"$ref": "#/definitions/elementProperties"
}
}
}
}
]
}
}
}
},
"tools": {
"type": "array",
"description": "Tools used by the module",
Expand All @@ -158,17 +40,17 @@
"homepage": {
"type": "string",
"description": "Homepage of the tool",
"pattern": "^(http|https)://.*$"
"pattern": "^https?://.*$"
},
"documentation": {
"type": "string",
"description": "Documentation of the tool",
"pattern": "^(http|https|ftp)://.*$"
"pattern": "^(https?|ftp)://.*$"
},
"tool_dev_url": {
"type": "string",
"description": "URL of the development version of the tool's documentation",
"pattern": "^(http|https)://.*$"
"pattern": "^https?://.*$"
},
"doi": {
"description": "DOI of the tool",
Expand All @@ -194,17 +76,9 @@
"message": "Licence must be an array of one or more entries, e.g. [\"MIT\"]"
},
"identifier": {
"type": "string",
"description": "bio.tools identifier of the tool",
"anyOf": [
{
"type": "string",
"pattern": "^biotools:.*$"
},
{
"type": "string",
"maxLength": 0
}
]
"pattern": "^(biotools:.*)?$"
}
},
"required": ["description"],
Expand All @@ -225,9 +99,134 @@
}
}
}
},
"extra_args": {
"type": "array",
"description": "Extra arguments for the module",
"items": {
"type": "object",
"properties": {
"description": {
"type": "string",
"description": "Description of the argument"
}
}
}
},
"input": {
"type": "array",
"description": "Input channels for the module",
"items": {
"oneOf": [
{
"$ref": "#/definitions/channelElement"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/channelElement"
}
}
]
}
},
"output": {
"type": "object",
"description": "Output channels for the module",
"patternProperties": {
".*": {
"$ref": "#/definitions/channelArray"
}
}
},
"topics": {
"type": "object",
"description": "Topics of the module",
"patternProperties": {
".*": {
"$ref": "#/definitions/channelArray"
}
}
},
"authors": {
"type": "array",
"description": "Authors of the module",
"items": {
"type": "string"
}
},
"maintainers": {
"type": "array",
"description": "Maintainers of the module",
"items": {
"type": "string"
}
},
"containers": {
"type": "object",
"description": "Container images for the module",
"properties": {
"docker": {
"type": "object",
"description": "Docker containers for different architectures",
"additionalProperties": {
"$ref": "#/definitions/container"
}
},
"singularity": {
"type": "object",
"description": "Singularity containers for different architectures",
"additionalProperties": {
"allOf": [
{
"$ref": "#/definitions/container"
},
{
"properties": {
"name": {
"pattern": "^oras://.*$"
}
},
"required": ["https"]
}
]
}
},
"conda": {
"type": "object",
"description": "Conda lock files for different architectures",
"additionalProperties": {
"$ref": "#/definitions/condaLockFile"
}
}
}
}
},
"definitions": {
"channelElement": {
"type": "object",
"patternProperties": {
".*": {
"$ref": "#/definitions/elementProperties"
}
}
},
"channelArray": {
"type": "array",
"items": {
"oneOf": [
{
"$ref": "#/definitions/channelElement"
},
{
"type": "array",
"items": {
"$ref": "#/definitions/channelElement"
}
}
]
}
},
"elementProperties": {
"type": "object",
"properties": {
Expand Down Expand Up @@ -261,13 +260,49 @@
"patternProperties": {
".*": {
"type": "string",
"pattern": "^(http|https)://.*"
"pattern": "^https?://.*"
}
}
}
}
},
"required": ["type", "description"]
},
"container": {
"type": "object",
"description": "Container information for Docker or Singularity",
"properties": {
"name": {
"type": "string",
"description": "Container name/URI"
},
"https": {
"type": "string",
"description": "HTTPS URL to download the container (only for Singularity)",
"pattern": "^https://.*$"
},
"build_id": {
"type": "string",
"description": "Build ID of the container"
},
"scan_id": {
"type": "string",
"description": "Security scan ID of the container (only for Docker)"
}
},
"required": ["name", "build_id"]
},
"condaLockFile": {
"type": "object",
"description": "Conda lock file information",
"properties": {
"lock file": {
"type": "string",
"description": "URL to the conda lock file",
"pattern": "^https://.*$"
}
},
"required": ["lock file"]
}
},
"required": ["name", "description", "keywords", "authors", "output", "tools"]
Expand Down
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