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| Original file line number | Diff line number | Diff line change |
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| # Additional BCO configuration | ||
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| *New in version 1.3.0* | ||
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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` | ||
| - `prov.formats.bco.execution_domain.external_data_endpoints` | ||
| - `prov.formats.bco.execution_domain.environment_variables` | ||
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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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| *NOTE: The `environment_variables` setting differs from the BCO standard in that it only specifies the variable names. Only the variables specified in this list will be populated in the BCO, if they are present in the execution environment.* | ||
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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": "hadley_king@gwu.edu", | ||
| "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": "Eric.Donaldson@fda.hhs.gov", | ||
| "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" | ||
| ] | ||
| ] | ||
| } | ||
| execution_domain { | ||
| external_data_endpoints = [ | ||
| [ | ||
| "url": "protocol://domain:port/application/path", | ||
| "name": "generic name" | ||
| ], | ||
| [ | ||
| "url": "ftp://data.example.com:21/", | ||
| "name": "access to ftp server" | ||
| ], | ||
| [ | ||
| "url": "http://eutils.ncbi.nlm.nih.gov/entrez/eutils", | ||
| "name": "access to e-utils web service" | ||
| ] | ||
| ] | ||
| environment_variables = ["HOSTTYPE", "EDITOR"] | ||
| } | ||
| } | ||
| } | ||
| } | ||
| ``` | ||
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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 | ||
| } | ||
| execution_domain { | ||
| external_data_endpoints = params.bco_execution_domain_external_data_endpoints | ||
| environment_variables = params.bco_execution_domain_environment_variables | ||
| } | ||
| } | ||
| } | ||
| } | ||
| ``` | ||
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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": [ | ||
| // ... | ||
| ], | ||
| "bco_execution_domain_external_data_endpoints": [ | ||
| // ... | ||
| ], | ||
| "bco_execution_domain_environment_variables": [ | ||
| // ... | ||
| ] | ||
| } | ||
| ``` |
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| # Additional WRROC configuration | ||
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| *New in version 1.4.0* | ||
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| The `wrroc` format supports additional options to configure certain aspects of the Workflow Run RO-Crate. These fields cannot be inferred automatically from the pipeline or the run, and so must be entered through the config. | ||
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| The following config options are supported: | ||
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| - `prov.formats.wrroc.agent.contactType` | ||
| - `prov.formats.wrroc.agent.email` | ||
| - `prov.formats.wrroc.agent.name` | ||
| - `prov.formats.wrroc.agent.orcid` | ||
| - `prov.formats.wrroc.agent.phone` | ||
| - `prov.formats.wrroc.agent.ror` | ||
| - `prov.formats.wrroc.organization.contactType` | ||
| - `prov.formats.wrroc.organization.email` | ||
| - `prov.formats.wrroc.organization.name` | ||
| - `prov.formats.wrroc.organization.phone` | ||
| - `prov.formats.wrroc.organization.ror` | ||
| - `prov.formats.wrroc.license` | ||
| - `prov.formats.wrroc.publisher` | ||
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| Refer to the [WRROC User Guide](https://www.researchobject.org/workflow-run-crate/) for more information about the associated RO-Crate entities. | ||
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| Here is an example config: | ||
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| ```groovy | ||
| prov { | ||
| formats { | ||
| wrroc { | ||
| agent { | ||
| name = "John Doe" | ||
| orcid = "https://orcid.org/0000-0000-0000-0000" | ||
| email = "john.doe@example.org" | ||
| phone = "(0)89-99998 000" | ||
| contactType = "Researcher" | ||
| } | ||
| organization { | ||
| name = "University of XYZ" | ||
| ror = "https://ror.org/000000000" | ||
| } | ||
| license = "https://spdx.org/licenses/MIT" | ||
| publisher = "https://ror.org/000000000" | ||
| } | ||
| } | ||
| } | ||
| ``` |
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