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---|---|---|
@@ -1,9 +1,7 @@ | ||
{ | ||
"target_genomes": [ | ||
{ | ||
"sample": "example", | ||
"vcf_path": "/path/to/genome.vcf.gz", | ||
"chrom": 22 | ||
} | ||
] | ||
} | ||
[ | ||
{ | ||
"sample": "example", | ||
"vcf_path": "/path/to/genome.vcf.gz", | ||
"chrom": 22 | ||
} | ||
] |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,6 +1,4 @@ | ||
{ | ||
"nxf_params_file": { | ||
"scorefile": "/path/to/scorefile.txt", | ||
"format": "json" | ||
} | ||
"scorefile": "/path/to/scorefile.txt", | ||
"format": "json" | ||
} |
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---|---|---|
@@ -0,0 +1 @@ | ||
[{"sample":"cineca_synthetic_subset","vcf_path":null,"chrom":22,"bed":"https:\/\/gitlab.ebi.ac.uk\/nebfield\/test-datasets\/-\/raw\/master\/pgsc_calc\/cineca_synthetic_subset.bim","bim":"https:\/\/gitlab.ebi.ac.uk\/nebfield\/test-datasets\/-\/raw\/master\/pgsc_calc\/cineca_synthetic_subset.bed","fam":"https:\/\/gitlab.ebi.ac.uk\/nebfield\/test-datasets\/-\/raw\/master\/pgsc_calc\/cineca_synthetic_subset.fam"}] |
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@@ -1,39 +1,74 @@ | ||
{ | ||
"$schema": "http://json-schema.org/draft-07/schema", | ||
"$id": "https://raw.githubusercontent.com/nf-core/pgscalc/master/assets/schema_input.json", | ||
"title": "nf-core/pgscalc pipeline - params.input schema", | ||
"description": "Schema for the file provided with params.input", | ||
"type": "array", | ||
"items": { | ||
"type": "object", | ||
"properties": { | ||
"sample": { | ||
"type": "string", | ||
"pattern": "^\\S+$", | ||
"errorMessage": "Sample name must be provided and cannot contain spaces" | ||
}, | ||
"fastq_1": { | ||
"type": "string", | ||
"pattern": "^\\S+\\.f(ast)?q\\.gz$", | ||
"errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" | ||
}, | ||
"fastq_2": { | ||
"errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'", | ||
"anyOf": [ | ||
{ | ||
"type": "string", | ||
"pattern": "^\\S+\\.f(ast)?q\\.gz$" | ||
}, | ||
{ | ||
"type": "string", | ||
"maxLength": 0 | ||
} | ||
] | ||
} | ||
}, | ||
"required": [ | ||
"sample", | ||
"fastq_1" | ||
"$schema": "http://json-schema.org/draft-07/schema", | ||
"$id": "https://raw.githubusercontent.com/pgscatalog/pgsc_calc/master/assets/schema_input.json", | ||
"title": "Input schema", | ||
"description": "Schema for the file provided with params.input", | ||
"type": "array", | ||
"uniqueItems": true, | ||
"minItems": 1, | ||
"items": { | ||
"type": "object", | ||
"properties": { | ||
"sample": { | ||
"type": "string", | ||
"pattern": "^\\S+$", | ||
"errorMessage": "Sample name must be provided and cannot contain spaces" | ||
}, | ||
"vcf_path": { | ||
"type": "string", | ||
"pattern": "^\\S+\\.vcf\\.gz$", | ||
"errorMessage": "VCF path must end with .vcf.gz, mutually exclusive with bfile_path", | ||
"anyOf": [ | ||
{ | ||
"type": "string", | ||
"pattern": "^\\S+\\.vcf\\.gz$" | ||
}, | ||
{ | ||
"type": "string", | ||
"maxLength": 0 | ||
} | ||
] | ||
}, | ||
"bfile_path": { | ||
"errorMessage": "Plink 1 binary fileset prefix, must not end with bed / bim / fam, mutually exclusive with vcf_path", | ||
"anyOf": [ | ||
{ | ||
"type": "string", | ||
"pattern": "^\\S+$" | ||
}, | ||
{ | ||
"type": "string", | ||
"maxLength": 0 | ||
} | ||
] | ||
}, | ||
"chrom": { | ||
"errorMessage": "Plink 1 binary fileset prefix, must not end with bed / bim / fam, mutually exclusive with vcf_path", | ||
"anyOf": [ | ||
{ | ||
"type": "null" | ||
}, | ||
{ | ||
"type": "integer", | ||
"exclusiveMinimum": 1, | ||
"maximum": 22 | ||
} | ||
] | ||
} | ||
}, | ||
"required": [ | ||
"sample", | ||
"chrom" | ||
], | ||
"not": { | ||
"anyOf": [ | ||
{ | ||
"required": [ | ||
"vcf_path", | ||
"bfile_path" | ||
] | ||
} | ||
] | ||
} | ||
} | ||
} |
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