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Update json for meta yml #6669

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Update json for meta yml #6669

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7222c71
update JSON schema for modules meta.yml
mirpedrol Jun 19, 2024
d62d503
add identifier and ontologies to the modules meta.yml JSON schema
mirpedrol Jun 21, 2024
e3bcc10
remove qualifier
mirpedrol Jul 4, 2024
fb8761a
Conda remove defaults channel - structural changes (#5847)
ewels Aug 15, 2024
bb92ca2
Update `branch_update_staging` (#6657)
ewels Sep 17, 2024
f042fc9
Merge branch 'batch_update_staging' into update-json-for-meta-yml
ewels Sep 17, 2024
ecbda06
merge master branch
mirpedrol Sep 19, 2024
dc77451
[automated] Fix linting with Prettier
nf-core-bot Sep 19, 2024
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119 changes: 56 additions & 63 deletions modules/meta-schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -38,76 +38,16 @@
"type": "array",
"description": "Input channels for the module",
"items": {
"type": "object",
"patternProperties": {
".*": {
"type": "object",
"properties": {
"type": {
"type": "string",
"description": "Type of the input channel",
"enum": ["map", "file", "directory", "string", "integer", "float", "boolean", "list"]
},
"description": {
"type": "string",
"description": "Description of the input channel"
},
"pattern": {
"type": "string",
"description": "Pattern of the input channel, given in Java glob syntax"
},
"default": {
"type": ["string", "number", "boolean", "array", "object"],
"description": "Default value for the input channel"
},
"enum": {
"type": "array",
"description": "List of allowed values for the input channel",
"items": {
"type": ["string", "number", "boolean", "array", "object"]
},
"uniqueItems": true
}
},
"required": ["type", "description"]
}
}
"type": "array",
"items": { "$ref": "#/definitions/elementProperties" }
}
},
"output": {
"type": "array",
"description": "Output channels for the module",
"items": {
"type": "object",
"patternProperties": {
".*": {
"type": "object",
"properties": {
"type": {
"type": "string",
"description": "Type of the output channel",
"enum": ["map", "file", "directory", "string", "integer", "float", "boolean", "list"]
},
"description": {
"type": "string",
"description": "Description of the output channel"
},
"pattern": {
"type": "string",
"description": "Pattern of the input channel, given in Java glob syntax"
},
"enum": {
"type": "array",
"description": "List of allowed values for the output channel",
"items": {
"type": ["string", "number", "boolean", "array", "object"]
},
"uniqueItems": true
}
},
"required": ["type", "description"]
}
}
"items": { "$ref": "#/definitions/elementProperties" }
}
},
"tools": {
Expand Down Expand Up @@ -160,6 +100,11 @@
"minItems": 1,
"uniqueItems": true,
"message": "Licence must be an array of one or more entries, e.g. [\"MIT\"]"
},
"identifier": {
"type": "string",
"description": "bio.tools identifier of the tool",
"pattern": "^biotools:.*$"
}
},
"required": ["description"],
Expand All @@ -182,5 +127,53 @@
}
}
},
"definitions": {
"elementProperties": {
"type": "object",
"patternProperties": {
".*": {
"type": "object",
"properties": {
"type": {
"type": "string",
"description": "Type of the channel element",
"enum": ["map", "file", "directory", "string", "integer", "float", "boolean", "list"]
},
"description": {
"type": "string",
"description": "Description of the channel"
},
"pattern": {
"type": "string",
"description": "Pattern of the channel, given in Java glob syntax"
},
"enum": {
"type": "array",
"description": "List of allowed values for the channel",
"items": {
"type": ["string", "number", "boolean", "array", "object"]
},
"uniqueItems": true
},
"ontologies": {
"type": "array",
"description": "List of ontologies for the channel",
"uniqueItems": true,
"items": {
"type": "object",
"patternProperties": {
".*": {
"type": "string",
"pattern": "^(http|https)://.*"
}
}
}
}
},
"required": ["type", "description"]
}
}
}
},
"required": ["name", "description", "keywords", "authors", "output", "tools"]
}
56 changes: 28 additions & 28 deletions modules/nf-core/samtools/view/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@
"bam_bai": {
"content": [
[

]
],
"meta": {
Expand All @@ -44,7 +44,7 @@
"bam_stub_bai": {
"content": [
[

]
],
"meta": {
Expand All @@ -68,7 +68,7 @@
"cram_to_bam_index_cram": {
"content": [
[

]
],
"meta": {
Expand All @@ -80,7 +80,7 @@
"cram_to_bam_sam": {
"content": [
[

]
],
"meta": {
Expand All @@ -92,7 +92,7 @@
"cram_to_bam_index_sam": {
"content": [
[

]
],
"meta": {
Expand All @@ -104,7 +104,7 @@
"cram_crai": {
"content": [
[

]
],
"meta": {
Expand All @@ -116,7 +116,7 @@
"cram_csi": {
"content": [
[

]
],
"meta": {
Expand All @@ -128,7 +128,7 @@
"cram_to_bam_cram": {
"content": [
[

]
],
"meta": {
Expand All @@ -150,7 +150,7 @@
"bam_stub_sam": {
"content": [
[

]
],
"meta": {
Expand Down Expand Up @@ -182,7 +182,7 @@
"bam_csi": {
"content": [
[

]
],
"meta": {
Expand All @@ -194,7 +194,7 @@
"cram_to_bam_crai": {
"content": [
[

]
],
"meta": {
Expand All @@ -206,7 +206,7 @@
"cram_to_bam_index_crai": {
"content": [
[

]
],
"meta": {
Expand Down Expand Up @@ -262,7 +262,7 @@
"cram_to_bam_bai": {
"content": [
[

]
],
"meta": {
Expand All @@ -286,7 +286,7 @@
"cram_bam": {
"content": [
[

]
],
"meta": {
Expand All @@ -298,7 +298,7 @@
"bam_stub_cram": {
"content": [
[

]
],
"meta": {
Expand All @@ -310,7 +310,7 @@
"cram_to_bam_index_qname_bai": {
"content": [
[

]
],
"meta": {
Expand All @@ -322,7 +322,7 @@
"cram_to_bam_index_qname_crai": {
"content": [
[

]
],
"meta": {
Expand All @@ -334,7 +334,7 @@
"cram_bai": {
"content": [
[

]
],
"meta": {
Expand All @@ -346,7 +346,7 @@
"bam_stub_crai": {
"content": [
[

]
],
"meta": {
Expand Down Expand Up @@ -380,7 +380,7 @@
"cram_to_bam_index_qname_cram": {
"content": [
[

]
],
"meta": {
Expand All @@ -392,7 +392,7 @@
"bam_crai": {
"content": [
[

]
],
"meta": {
Expand All @@ -404,7 +404,7 @@
"bam_cram": {
"content": [
[

]
],
"meta": {
Expand All @@ -416,7 +416,7 @@
"cram_to_bam_csi": {
"content": [
[

]
],
"meta": {
Expand All @@ -428,7 +428,7 @@
"cram_sam": {
"content": [
[

]
],
"meta": {
Expand Down Expand Up @@ -462,7 +462,7 @@
"bam_sam": {
"content": [
[

]
],
"meta": {
Expand All @@ -474,7 +474,7 @@
"cram_to_bam_index_bai": {
"content": [
[

]
],
"meta": {
Expand All @@ -486,7 +486,7 @@
"cram_to_bam_index_qname_sam": {
"content": [
[

]
],
"meta": {
Expand All @@ -505,4 +505,4 @@
},
"timestamp": "2024-02-12T19:38:32.068596"
}
}
}
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