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Workflow output definition #275

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Workflow output definition #275

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9b3a10d
Add workflow output schema
bentsherman Feb 13, 2024
b03ed3b
Convert output schema to YAML
bentsherman Feb 28, 2024
b8dd9e2
Add output definition
bentsherman Feb 28, 2024
98b6574
Simplify output DSL, samplesheet generation
bentsherman Feb 28, 2024
5647bd1
Flatten output definition
bentsherman Feb 28, 2024
4405674
Fix bug
bentsherman Feb 28, 2024
47fa3f9
Add default publish mode
bentsherman Feb 29, 2024
ec29439
Add `toSamplesheet()` method to generate samplesheet
bentsherman Feb 29, 2024
48c6675
Move output file schemas to separate files
bentsherman Feb 29, 2024
9beb5ea
Add `schema` option to validate published outputs against a schema
bentsherman Feb 29, 2024
5b3587b
Replace process selectors with channel selectors
bentsherman Mar 19, 2024
9e8ef57
Use channel topics to reduce channel propagation
bentsherman Mar 27, 2024
35aaddd
Temporary workaround for topic operator bug
bentsherman Mar 28, 2024
77bdd19
Apply updates from upstream
bentsherman Mar 30, 2024
3ca8a28
Update using latest syntax
bentsherman Apr 10, 2024
bb7febb
Rename output -> publish
bentsherman Apr 24, 2024
c01bd0c
minor updates
bentsherman May 17, 2024
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125 changes: 125 additions & 0 deletions output_schema.json
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Original file line number Diff line number Diff line change
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{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/nf-core/fetchngs/master/output_schema.json",
"title": "nf-core/fetchngs pipeline outputs",
"description": "",
"type": "object",
"properties": {
"fastq": {
"type": "array",
"items": {
"type": "object",
"properties": {
"sample": {
"type": "string"
},
"fastq_1": {
"type": "string",
"format": "file-path",
"pattern": "^\\S+\\.f(ast)?q\\.gz$"
},
"fastq_2": {
"type": "string",
"format": "file-path",
"pattern": "^\\S+\\.f(ast)?q\\.gz$"
},
"run_accession": {
"type": "string"
},
"experiment_accession": {
"type": "string"
},
"sample_accession": {
"type": "string"
},
"secondary_sample_accession": {
"type": "string"
},
"study_accession": {
"type": "string"
},
"secondary_study_accession": {
"type": "string"
},
"submission_accession": {
"type": "string"
},
"run_alias": {
"type": "string"
},
"experiment_alias": {
"type": "string"
},
"sample_alias": {
"type": "string"
},
"study_alias": {
"type": "string"
},
"library_layout": {
"type": "string"
},
"library_selection": {
"type": "string"
},
"library_source": {
"type": "string"
},
"library_strategy": {
"type": "string"
},
"library_name": {
"type": "string"
},
"instrument_model": {
"type": "string"
},
"instrument_platform": {
"type": "string"
},
"base_count": {
"type": "integer"
},
"read_count": {
"type": "integer"
},
"tax_id": {
"type": "string"
},
"scientific_name": {
"type": "string"
},
"sample_title": {
"type": "string"
},
"experiment_title": {
"type": "string"
},
"study_title": {
"type": "string"
},
"sample_description": {
"type": "string"
},
"fastq_md5": {
"type": "string",
"pattern": "^[0-9a-f]{32}$"
},
"fastq_bytes": {
"type": "integer"
},
"fastq_ftp": {
"type": "string"
},
"fastq_galaxy": {
"type": "string"
},
"fastq_aspera": {
"type": "string"
}
},
"required": ["sample", "fastq_1"]
}
}
}
}