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| # Additional BCO configuration | ||
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| The `bco` format supports additional "pass-through" options for certain BCO fields. These fields cannot be inferred automatically from a pipeline or run, and so must be entered through the config. External systems can use these config options to inject fields automatically. | ||
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| The following config options are supported: | ||
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| - `prov.formats.bco.provenance_domain.review` | ||
| - `prov.formats.bco.provenance_domain.derived_from` | ||
| - `prov.formats.bco.provenance_domain.obsolete_after` | ||
| - `prov.formats.bco.provenance_domain.embargo` | ||
| - `prov.formats.bco.usability_domain` | ||
| - `prov.formats.bco.description_domain.keywords` | ||
| - `prov.formats.bco.description_domain.xref` | ||
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| These options correspond exactly to fields in the BCO JSON schema. Refer to the [BCO User Guide](https://docs.biocomputeobject.org/user_guide/) for more information about these fields. | ||
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| Here is an example config based on the BCO User Guide: | ||
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| ```groovy | ||
| prov { | ||
| formats { | ||
| bco { | ||
| provenance_domain { | ||
| review = [ | ||
| [ | ||
| "status": "approved", | ||
| "reviewer_comment": "Approved by GW staff. Waiting for approval from FDA Reviewer", | ||
| "date": "2017-11-12T12:30:48-0400", | ||
| "reviewer": [ | ||
| "name": "Charles Hadley King", | ||
| "affiliation": "George Washington University", | ||
| "email": "[email protected]", | ||
| "contribution": "curatedBy", | ||
| "orcid": "https://orcid.org/0000-0003-1409-4549" | ||
| ] | ||
| ], | ||
| [ | ||
| "status": "approved", | ||
| "reviewer_comment": "The revised BCO looks fine", | ||
| "date": "2017-12-12T12:30:48-0400", | ||
| "reviewer": [ | ||
| "name": "Eric Donaldson", | ||
| "affiliation": "FDA", | ||
| "email": "[email protected]", | ||
| "contribution": "curatedBy" | ||
| ] | ||
| ] | ||
| ] | ||
| derived_from = 'https://example.com/BCO_948701/1.0' | ||
| obsolete_after = '2118-09-26T14:43:43-0400' | ||
| embargo = [ | ||
| "start_time": "2000-09-26T14:43:43-0400", | ||
| "end_time": "2000-09-26T14:43:45-0400" | ||
| ] | ||
| } | ||
| usability_domain = [ | ||
| "Identify baseline single nucleotide polymorphisms (SNPs)[SO:0000694], (insertions)[SO:0000667], and (deletions)[SO:0000045] that correlate with reduced (ledipasvir)[pubchem.compound:67505836] antiviral drug efficacy in (Hepatitis C virus subtype 1)[taxonomy:31646]", | ||
| "Identify treatment emergent amino acid (substitutions)[SO:1000002] that correlate with antiviral drug treatment failure", | ||
| "Determine whether the treatment emergent amino acid (substitutions)[SO:1000002] identified correlate with treatment failure involving other drugs against the same virus", | ||
| "GitHub CWL example: https://github.com/mr-c/hive-cwl-examples/blob/master/workflow/hive-viral-mutation-detection.cwl#L20" | ||
| ] | ||
| description_domain { | ||
| keywords = [ | ||
| "HCV1a", | ||
| "Ledipasvir", | ||
| "antiviral resistance", | ||
| "SNP", | ||
| "amino acid substitutions" | ||
| ] | ||
| xref = [ | ||
| [ | ||
| "namespace": "pubchem.compound", | ||
| "name": "PubChem-compound", | ||
| "ids": ["67505836"], | ||
| "access_time": "2018-13-02T10:15-05:00" | ||
| ], | ||
| [ | ||
| "namespace": "pubmed", | ||
| "name": "PubMed", | ||
| "ids": ["26508693"], | ||
| "access_time": "2018-13-02T10:15-05:00" | ||
| ], | ||
| [ | ||
| "namespace": "so", | ||
| "name": "Sequence Ontology", | ||
| "ids": ["SO:000002", "SO:0000694", "SO:0000667", "SO:0000045"], | ||
| "access_time": "2018-13-02T10:15-05:00" | ||
| ], | ||
| [ | ||
| "namespace": "taxonomy", | ||
| "name": "Taxonomy", | ||
| "ids": ["31646"], | ||
| "access_time": "2018-13-02T10:15-05:00" | ||
| ] | ||
| ] | ||
| } | ||
| } | ||
| } | ||
| } | ||
| ``` | ||
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| Alternatively, you can use params to make it easier for an external system: | ||
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| ```groovy | ||
| prov { | ||
| formats { | ||
| bco { | ||
| provenance_domain { | ||
| review = params.bco_provenance_domain_review | ||
| derived_from = params.bco_provenance_domain_derived_from | ||
| obsolete_after = params.bco_provenance_domain_obsolete_after | ||
| embargo = params.bco_provenance_domain_embargo | ||
| } | ||
| usability_domain = params.bco_usability_domain | ||
| description_domain { | ||
| keywords = params.bco_description_domain_keywords | ||
| xref = params.bco_description_domain_xref | ||
| } | ||
| } | ||
| } | ||
| } | ||
| ``` | ||
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| This way, the pass-through options can be provided as JSON in a [params file](https://nextflow.io/docs/latest/reference/cli.html#run): | ||
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| ```jsonc | ||
| { | ||
| "bco_provenance_domain_review": [ | ||
| // ... | ||
| ], | ||
| "derived_from": "...", | ||
| "obsolete_after": "...", | ||
| "embargo": { | ||
| "start_time": "...", | ||
| "end_time": "..." | ||
| }, | ||
| "bco_usability_domain": [ | ||
| // ... | ||
| ], | ||
| "bco_description_domain_keywords": [ | ||
| // ... | ||
| ], | ||
| "bco_description_domain_xref": [ | ||
| // ... | ||
| ] | ||
| } | ||
| ``` |
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