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Batch update of modules #6674

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merged 9 commits into from
Sep 20, 2024
Merged

Batch update of modules #6674

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fb8761a
Conda remove defaults channel - structural changes (#5847)
ewels Aug 15, 2024
bb92ca2
Update `branch_update_staging` (#6657)
ewels Sep 17, 2024
c9caefa
update JSON schema for modules meta.yml (#5837)
mirpedrol Sep 19, 2024
a29c208
Bulk update meta yml modules (#6015)
mirpedrol Sep 20, 2024
e18b90c
Merge branch 'master' into batch_update_staging
mirpedrol Sep 20, 2024
95fb765
allow identifier to be an empty string
mirpedrol Sep 20, 2024
4a31965
run prettier
mirpedrol Sep 20, 2024
4e0b3a6
fixed indentation errors
mirpedrol Sep 20, 2024
9c8c21c
fix meta.yml of missing modules
mirpedrol Sep 20, 2024
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127 changes: 64 additions & 63 deletions modules/meta-schema.json
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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 +100,19 @@
"minItems": 1,
"uniqueItems": true,
"message": "Licence must be an array of one or more entries, e.g. [\"MIT\"]"
},
"identifier": {
"description": "bio.tools identifier of the tool",
"anyOf": [
{
"type": "string",
"pattern": "^biotools:.*$"
},
{
"type": "string",
"maxLength": 0
}
]
}
},
"required": ["description"],
Expand All @@ -182,5 +135,53 @@
}
}
},
"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"]
}
63 changes: 33 additions & 30 deletions modules/nf-core/abacas/meta.yml
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Expand Up @@ -14,40 +14,43 @@ tools:
documentation: http://abacas.sourceforge.net/documentation.html
doi: "10.1093/bioinformatics/btp347"
licence: ["GPL v2-or-later"]
identifier: biotools:abacas
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- scaffold:
type: file
description: Fasta file containing scaffold
pattern: "*.{fasta,fa}"
- fasta:
type: file
description: FASTA reference file
pattern: "*.{fasta,fa}"
- - meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- scaffold:
type: file
description: Fasta file containing scaffold
pattern: "*.{fasta,fa}"
- - fasta:
type: file
description: FASTA reference file
pattern: "*.{fasta,fa}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- results:
type: file
description: |
List containing abacas output files
[ 'test.abacas.bin', 'test.abacas.fasta', 'test.abacas.gaps',
'test.abacas.gaps.tab', 'test.abacas.nucmer.delta',
'test.abacas.nucmer.filtered.delta', 'test.abacas.nucmer.tiling',
'test.abacas.tab', 'test.abacas.unused.contigs.out',
'test.abacas.MULTIFASTA.fa' ]
pattern: "*.{abacas}*"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- "*.abacas*":
type: file
description: |
List containing abacas output files
[ 'test.abacas.bin', 'test.abacas.fasta', 'test.abacas.gaps',
'test.abacas.gaps.tab', 'test.abacas.nucmer.delta',
'test.abacas.nucmer.filtered.delta', 'test.abacas.nucmer.tiling',
'test.abacas.tab', 'test.abacas.unused.contigs.out',
'test.abacas.MULTIFASTA.fa' ]
pattern: "*.{abacas}*"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@joseespinosa"
- "@drpatelh"
Expand Down
54 changes: 29 additions & 25 deletions modules/nf-core/abricate/run/meta.yml
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Expand Up @@ -11,34 +11,38 @@ tools:
documentation: https://github.com/tseemann/abricate
tool_dev_url: https://github.com/tseemann/abricate
licence: ["GPL v2"]
identifier: biotools:ABRicate
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- assembly:
type: file
description: FASTA, GenBank or EMBL formatted file
pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}"
- databasedir:
type: directory
description: Optional location of local copy of database files, possibly with custom databases set up with `abricate --setupdb`
pattern: "*/"
- - meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- assembly:
type: file
description: FASTA, GenBank or EMBL formatted file
pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}"
- - databasedir:
type: directory
description: Optional location of local copy of database files, possibly with
custom databases set up with `abricate --setupdb`
pattern: "*/"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- report:
type: file
description: Tab-delimited report of results
pattern: "*.{txt}"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- "*.txt":
type: file
description: Tab-delimited report of results
pattern: "*.{txt}"
- versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@rpetit3"
maintainers:
Expand Down
45 changes: 24 additions & 21 deletions modules/nf-core/abricate/summary/meta.yml
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Expand Up @@ -11,30 +11,33 @@ tools:
documentation: https://github.com/tseemann/abricate
tool_dev_url: https://github.com/tseemann/abricate
licence: ["GPL v2"]
identifier: biotools:ABRicate
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reports:
type: file
description: FASTA, GenBank or EMBL formatted file
pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}"
- - meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reports:
type: file
description: FASTA, GenBank or EMBL formatted file
pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- report:
type: file
description: Tab-delimited report of aggregated results
pattern: "*.{txt}"
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- "*.txt":
type: file
description: Tab-delimited report of aggregated results
pattern: "*.{txt}"
- versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@rpetit3"
maintainers:
Expand Down
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